Most people that visit the San Juans arrive by Washington State Ferries which start in Anacortes. The islands get people from Sidney, Victoria and British Columbia too. Ferries are often crowded and its best to get there early so you can make sure the ferries are not overloaded. You can also park your car at the Anacortes car terminal, and load the ferry by foot. The problem is that except for Friday Harbor, where the ferry dock is right in town, there isn't much to see and do, when you arrive without transportation.
Air transportation is available from different
main land points to each of the larger islands. Some sources of
transportaiton is boat, car, air plane, ferry, bike and of course
just to walk. There are auto and bicycle rentals at the San Juans
that people can use to get around the island. If you don't like to
bicycle or drive a car then you go on a bus or walk.