most tour boats ( circle line etc ) do a cruise past, though again not very close to see them very well .
if you really want to see these places the best way is to actually go http://www.statuecruises.com/ is the official ticket seller .
they will get you the closest to see and visit
The SI Ferry is a quick trip. All told, it takes about an hour RT. If you are in the city for a short time, this is a worthwhile way to say you saw it , without spending a whole bunch of time on it. We went at night and were not looking for Ellis Island. I don't you can see it from the ferry.
The view of lower Manhattan at night is magical from the ferry, though..and it's free. For me, I guess it would depend on how much time I had
You can see both from the SI ferry but in the case of Ellis island you need to know what you are looking for and it is just an island with some ornate buildings on it. I still think that the official cruise even though you can't go into the statue is well worth the money and if you prebook you are only giving up a few more hours of your time. I find Ellis island one of the most interesting things to do in NYC.
It is important to notice that the Staten Island Ferry is basically a commuter boat. If you do decide to go to sightsee, stay away from Rush Hour, when it, like subways will be packed.
It docks at South Ferry which is at the southern tip of Manhattan. It runs hourly in the middle of the night, every 30 minutes during most of the day and more frequently during rush hours.
You can catch
the R train from whitehall st/south ferry to Court st or
the 4 or 5 line from bowling green to Borough Hall
I have done both and found it a easy walk and well sign posted to the Brooklyn Bridge
We did the SI ferry the first night we were there. I had to start my trip with seeing it, even from afar. But we had no doubt what we were seeing. Wish I could post a couple pics so you could see the distance.