New York City is served by three major airports, three smaller suburban airports, two major train stations and several interstate bus terminals.

By Air

John F. Kennedy International (JFK) is New York’s largest airport and the top international air passenger gateway in the United States. Located in the Queen’s borough, it is about 15 miles outside Manhattan, but traffic is often heavy and unpredicable.  NYC taxis offer a flat rate to/from Manhattan.  Depending on the traffic and time of day, the train is often the best option between Manhattan and JFK.  AirTrain stops at every JFK terminal and connects with both the NYC Subway (Howard Beach and Jamaica stations) and Long Island Railroad (Jamaica Station).

LaGuardia (LGA) is the closest to Midtown and Upper Manhattan, and thus preferred by some travelers. LaGuardia is largely a domestic airport, with some flights to/from Canada and limited long-distance flights.  It has the least convenient mass transit connections, but metered taxis are readily available and relatively cheap.  The #60 city bus from 106th and Broadway for $2.50 goes to LGA via Broadway, 125th St. and the Triborough Bridge directly to LGA and stops at all terminals.  There are also private buslines going from LGA to midtown for about $15.00.

Newark-Liberty International (EWR) in New Jersey is the closest to lower Manhattan. International flights into this hub can be cheaper than those to JFK.  The best route into Manhattan, especially at high traffic times of the day, is via New Jersey Transit trains, which runs frequently and quickly between the airport and New York's Pennsylvania station.  Newark's airport rail station is serviced by Newark AirTrain, which stops at every terminal.  Of the three larger NYC-area airports, taxis to/from Newark will cost the most and will often include excess fees given NYC taxis can't pick up passengers across state lines in Newark, and vice versa.

Macarthur Airport (ISP) in Islip, Long Island; Westchester County Airport (HPN) in White Plains; and Stewart Airport (SWF) in Newburgh are smaller suburban airports.

By Train

Travelers along the east coast corridor from Boston to Washington, D.C. usually find Amtrak the most efficient way to get to New York; reason is that you don't risk the flight delays common especially at Newark and La Guardia, or the traffic jams that make it advisable to leave ample time to get  between the city and its three airports.     

Amtrak, Long Island Railroad and New Jersey Transit trains run into Pennsylvania Station, directly under Madison Square Garden (at 7th or 8th Avenue between West 32nd and 33rd Streets). Popular trains fill up quickly during rush hour, so go online or call for reservations. You can grab your ticket at one of the station’s electronic kiosks. 

Visitors from Westchester and Connecticut can take Metro North rail lines into the beautifully restored Grand Central Terminal in Midtown at 42nd Street and Park Avenue. An architectural treasure and tourist attraction in itself, Grand Central Terminal is home to a variety of upscale eateries and shops.

By Bus

Many regional bus services use the Port Authority Bus Terminal on 8th Avenue and West 41st and 42nd Streets.  Visitors from Massachusetts, Rhode Island, Connecticut, New Jersey, Pennsylvania or Delaware might consider Peter Pan, one of the terminal’s oldest discount bus services. For frequent service from Boston, Buffalo, Toronto, Atlantic City, Philadelphia, Baltimore or Washington, many opt for Megabus. Frugal riders can compromise comfort for a $15 (or cheaper) ticket on “Chinese Buses” that arrive and depart in Chinatown. The comfortable Hampton Jitney serves Long Island visitors and the Hampton Luxury Liner goes to and from the Hamptons.

By Car

New York’s highways allow relatively easy access to the heart of Manhattan, but heavy traffic can make driving an intimidating experience. It’s difficult to find parking within the city and usually expensive if you do. Getting to New York City by car is not recommended.

By Boat

New York City is an important passenger seaport, and travelers can arrive in luxury on ocean liners or cruise ships, including the Luxurious British Liners like the Grand RMS Queen Mary 2.

Getting Downtown 

Visitors can navigate from the airport to the city via public transportation, cabs, shuttle buses or car rentals. If you flew into JFK, a free and reliable service-desk can help you sort through the options and book ground transportation arrangements.

Public Transit*

From JFK, use Airtrain ($5 per person, plus $1 if you need a new MetroCard) to get from terminals to subways or the Long Island Railroad. Airtrain’s Howard Beach line connects to the A train, which runs through Queens and Brooklyn before entering lower Manhattan; its Jamaica branch goes to Jamaica station, Queens, where you can connect to either the Long Island Railroad (LIRR) or the E or J/Z subway lines into Manhattan.

From Newark, Airtrain travels to NJ Transit Northeast corridor railroad line, which goes to Penn Station. For those on a tight budget (and not in a rush), use the PATH, aka the Hudson Tubes, formally known as the Port Authority Trans Hudson Lines. You will probably have to make subway or bus transfers so this option is time consuming (up to two hours of travel), but it only costs $4.75 total.

From LGA, the least expensive way (and often the fastest) to Manhattan is via  the M60 bus, or the Q70 or Q48 buses. Basic fare is $2.50 per person. You will need to use coins or buy a MetroCard in advance of getting on the bus, because city buses do not accept bills. See this MTA webpage for bus and subway details for JFK and LGA. Metrocards are sold at LaGuardia Airport. The M60 stops at all terminals and at the Astoria Blvd Station of the N and Q trains in Queens before going along 125 St in Manhattan and stopping at four different subway lines in Manhattan. The others go for shorter distances to subway stations in Queens.

Note that the Q33, no longer goes to LGA; that service has been replaced by the Q70 Limited bus, which stops at "61 St.-Woodside Station" on the 7 and <7> express (as well as the Long Island Railroad), and at "74th St-Bway" (Queens) on the 7 local, which is the same station as "Roosevelt Avenue-Jackson Heights" on the E, F, M, R trains of the Queens Blvd.  line. After those two station stops, the Q70 bus runs non-stop on a highway right into the Airport. Note that the Q70 does not stop at the Marine Air Terminal; but the Q47 from Jackson Hts and the Q48 from 111 St (Queens) on the 7 line still stop there.

To go from LGA to JFK, take the Q70 bus to the first stop off the airport. (Jackson Heights), take the Jamaica-bound E train to "Sutphin-JFK", and the JFK Air Train to the terminals (for a total price of $7.50).

*More public transit details listed below.

Cabs

Official taxi lines are outside each of the terminals.  From JFK or Newark to anywhere in Manhattan, taxis are fixed rates ($52.50 from JFK and $50 from Newark, plus tip and tolls). Taxis from LGA run on the meter so fares will be affected by heavy traffic; it usually costs $20-$25 to reach Upper or Mid Manhattan and $25-$30 to get to Lower Manhattan.

If you decide to invest in a cab, only use official NYC Yellow Taxis from the taxi dispatcher or a pre-arranged car service. It is illegal for livery cars, Lincoln Town Car (“black car”) services or limousine drivers to solicit you at the terminals; these drivers run scams and will ask for more money once you arrive at your destination.  However, booking a car service in advance (using a service like Dial7 or Groundlink) can add some convenience to your trip.  Cars can be booked and paid in advance.  You can also request that the driver meet you at baggage claim to help with luggage. If traveling solo or in a small group, a  new online platform, "Cab With Me" allows New Yorkers to find other people nearby with whom they can share the taxi and save money.

Shuttle buses

JFK, La Guardia and Newark all have shared van rides into the city. It’s less expensive than a cab if you’re traveling alone, but it takes longer because you may need to stop at other hotels or addresses before arriving at your destination. From LGA or JFK, the Airport Express bus service goes to several locations for $13-$16 one-way.  The NYC Airporter also provides shuttle service to and from LGA-Manhattan and to and from JFK-Manhattan for about $13.00 one-way.  Be warned, GoAirlink Shuttle gets terrible reviews.

Car rental

With heavy traffic and limited parking, NYC is not an easy place to drive, and if you rent a car, you’ll probably leave it parked in the lot. Unless you are planning extensive travel outside of New York City itself, renting a car is a waste of time and money.  

If you do need a rental car for travel to areas that are not well served by public transit, use a general travel booking site that can compare rates from various car rental agencies  

Taking a train to a station outside of NYC and renting a car there can be more affordable and less stressful than picking up a car in NYC.  The best options will depend on where you are ultimately traveling with the car, and whether you intend to return to NYC when you are through.

Getting Around

The Metropolitan Transit Authority (MTA) operates subways and buses that can get you anywhere in the city, though you can also walk or take a cab. Note that “uptown” means north and “downtown” means south.

Walking 

New York City is one of the world’s best walking cities. The sidewalks pulse with energy, and you might even stroll past movie stars, television personalities, music icons or models. Twenty blocks (e.g. 40th St to 60th St) is about a mile and usually takes 20 – 30 minutes to walk.  You can generally get anywhere in Midtown Manhattan within an hour.

If you're exploring Greenwich Village, SoHo and TriBeCa, grab a map or ask for directions. But all of Manhattan north of 14th Street is laid out on an easy-to-navigate grid, with Avenues running North-South and numbered streets running East-West. 

Subway

New York’s subway system is the fastest way to get around the city, and if you're traveling alone it's probably the most economical. MetroCards can be purchased at many stores and newsstands above ground, or buy one at kiosks inside the station. Single rides cost $2.25, but opt for a day-pass or 10-ride pass if you plan to travel a lot during your visit. Infants and children less than 44 inches tall can ride for free. In October 2012 a week-long metrocard gave an adult unlimited travel on all subways and all buses for $29, very economical for a tourist wanting to go all over the city all day long for a week. Buy at subway station machines. Included is partway from Manhattan to JFK, an extra $5 at Jamaica to airport.

Most NY subway trunks are four track - there are local trains that make every stop, and expresses that only make some stops. It's important to know which you want, or you will waste a lot of time backtracking. In most stations the locals are on the outside tracks, and the expresses on the inner tracks. But there are some exceptions, so look for the signs above the platform and listen to announcements

Once you're on the subway, you can transfer as many times as you want. Plan local public transportation using Publicroutes.com or Hopstop.com. Both websites provide excellent online directions in and around the city.

The Lexington Avenue Lines (4, 5, 6) run north/south on the East Side and are helpful if you’re going to the Metropolitan Museum of Art, the Guggenheim Museum, the Statue of Liberty, Yankee Stadium and Chinatown.

The Seventh Avenue Lines (1, 2, 3) run north/south along Broadway and then Seventh Avenue. It can help you reach the West Village, Chelsea, Tribeca neighborhoods and ferries to Staten Island.

The Eighth Avenue Lines (A, C, E) runs north/south on the West Side and can take you near the Natural History Museum, the west side of Central Park and JFK Airport.

The Sixth Avenue Line (B, D, F, M) runs north/south through Manhattan for access to the Museum of Modern Art, Rockefeller Center, Radio City Music Hall and St. Patrick’s Cathedral. Some lines run east to Brooklyn or Queens.

The Broadway Lines (N, Q, R) go down Broadway below 42nd Street and on Seventh Avenue above Times Square. They can help you get to Chinatown, SoHo, New York University, Union Square, the Empire State Building, Carnegie Hall and Central Park, as well as the Financial District and Brooklyn.

Buses

Bus routes thoroughly cover all major areas of the city and, while not as fast as the subway system, they provide an inexpensive alternative to cabs and another great way to encounter everyday folks. Pay with a MetroCard or change; fare boxes don’t accept bills.

The route designations include a letter and number. The letter is the borough: M=Manhattan Q=Queens B=Brooklyn Bx=Bronx and S=Staten Island. Most routes stay within the borough, but there are exceptions such as the Q32 that goes to Penn Station in Manhattan. Express buses for commuters are marked with an X above the window; these cost more and most visitors won’t have any use for them.

Boats & Ferry Service

For excellent views of Lady Liberty, Ellis Island or skyscrapers, take the Staten Island Ferry, a free commuter ferry that operates year-round between St. George on Staten Island and Whitehall Street in Lower Manhattan. When you get to Staten Island you must get off the boat, but if the weather is nice you might take a stroll along the waterfront promenade or watch giant cargo ships glide by.  Note: the Staten Island Ferry does not actually stop at the Statue of Liberty or Ellis Island.

Statue Cruises also operate ferries to Lady Liberty and Ellis Island, but you have to buy a ticket. Advanced purchase online is highly recommended, though you can get same-day tickets at Castle Clinton.

Bicycle

When the weather is nice, rent a bicycle and ride along the Hudson River path or through Central Park. Popular bike tour and rentals include Central Park Bicycle Tour and Rental; Toga Bike Shop, located conveniently between the Hudson and Central Park; and Gotham Bikes Downtown, not far from the Hudson. A tour company called Bike the Apple also offers guided bicycle tours in all five boroughs.

Taxi Cabs

If you’re traveling in a group of two or more, this is probably the best way to travel in New York City. You can easily get anywhere in Manhattan for no more than $10 - $15, less than a subway ride when split between a group. Ask your hotel concierge or a doorman to call a taxi for you, or just head to the street and raise a hand in the air. Real NYC taxis are yellow with a metal seal on the hood, a meter for billing, a divider inside the car and special taxi license plates. Look for one with a lit light on top but no “off duty” mark.

Commuter Rail

Commuter rails go between the city and its suburbs, though you can use them for intracity transit, too, since some tourist destinations are closer to their stops than the subway. The Long Island Railroad runs from Penn Station to Queens and Brooklyn, while Metro-North Railroad provides service from Grand Central Terminal to the Bronx and north suburbs. MetroCards aren’t valid on these trains, so buy a separate ticket online or in the stations before you board.

Information source about New York Travel Phone Apps from the MTA dot info