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San Juan Island is the most diverse. Using it as a base, you can take the inter-island ferry to explore Lopez, Orcas and Shaw Islands . Each has features worth at least reading about on the web. See the website of the San Juan Islands VIsitors Bureau for detailed island information and transportation options for getting there: http://www.visitsanjuans.com/
Check also the Overview and Things to Do tabs for each of the San Juan Islands for details.
A personal or rented vehicle is the most flexible way to see San Juan Island sights if you wish to set your own pace. San Juan Transit Company can provide a variety of rides and tours. http://sanjuantransit.com/
SJI has the most accessible waterfront, two national parks - each very different, Lime Kiln Point State Park with lovely views of the Straits and possible/probable marine mammal sightings. Friday Harbor is the town, and offers a Whale Museum , galleries, shops, large marina and more.
Roche Harbor offers a marina, an historic hotel, restaurants, garden grounds.
Nearby, see the Westcott Bay Preserve - an outdoor sculpture park.- extremely well done and scenic.
Everywhere you drive, scenery including foxes, rabbits, deer, raptors, especially at American Camp.
And opposite the winery, Mona the Camel!
Orcas offers Mt. Constitution ; you can drive or hike it (quite steep) to the top. At which, a climable tower. A terrific view.
Lopez is a well known biking island, gentle roads, scenic locations, people always wave from their vehicles when you pass each other. You can rent bikes on the island.
Shaw offers much less, and you will fill your time with the first one if not Orcas and Lopez.
Lonesome Cove Resort on SJI is a dream; no TV, no phones, on the water, lovely grounds. Suggest checking the accommodations/lodging section of their website to see what appeals to you or meets your needs.Y
Check the Washington State Ferry schedule and time yourselves accordingly. See this, but get updates near your trip: http://www.wsdot.wa.gov/ferries/sched...
If It's tourist season, you will want to be at the Anacortes ferry dock at least an hour before boarding. Call the ferry folks when you arrive and inquire. For your return, it is critical that you check with the ferry dock folks and inquire when you should leave your car in the assigned lanes so you can catch the ferry to Anacortes. While the car sits, you can walk around Friday Harbor , have a decent meal, kill time. Trust the writer on this point.
Lastly, Spring and Summer have long days up here, so you will have plenty of time to see a lot.