I love San Juan Island and like staying in Friday Harbor. For $20? they have a hop on hop off shuttle bus that takes you to various sights on the island, like a lavendar farm, winery, state parks often with naturalist on sight for orca spotting, Roche Harbor (great for lunch) and other points of interest. We stayed at Friday's Historic Inn and found it to be fine for an overnight. It's 2 blocks from the ferry dock, so it is very easy to walk to the hotel, and there are lots of restaurants and shops in the area.

You might want to also look into flying into Bellingham (80 miles north of Seattle, and 45 miles from Vancouver) and taking the walk on boat that goes to the various San Juan islands as well as Victoria. Their website is www.whales.com and we took them last year to Victoria. The captain was great and very informative about life on the islands and history. It is much easier to take them to San Juan island and they don't have all the traffic jams and delays that they do in Anacortes. There is on sight overnight parking at the B'ham ferry terminal, and it is very convenient. They also go to Victoria from Friday Harbor, so they might have a deal if you go to variuos islands with them. I highly recommend looking into this option.

Have a great trip. The San Juan Islands are gorgeous and should not be missed!