Where to go at the San Juan Islands? : Seattle: "First of all, it's a great time of year to get up there and queitly enjoy the place without crowds.
If you go to San Juan Island, you can get away without driving you car onto the ferry. This would allow you to explore the town of Friday Harbor, but you would be limited from exploring the further out places like american and english camp as well as lime kiln park. Orca sightings are possible from Limn Kiln where they have a whale research station, but not totally common this time of year. I really like the Front Street Brewery in Friday Harbor.
Orcas Island is worth considering if you like hiking or views from high points. Mt Constitution in Moran State Park is a little over 2000 feet overlooking all of the San Juans. You can drive to the top or stop and explore the many trails around the Mt.
On the way up or down to the area, consider taking the ferry from Mukilteo to Clinton and driving up Whidbey Island. It takes about an hour more, but is a lot more relaxing and beautiful than I-5. You would arrive onto the SE corner of Fidalgo Island via Deception Pass and then continue on towards the ferry which is on the NW part of Fidalgo.
Don't overlook Anacortes on the way to or from the ferry. Some great places for food and drink: Adrift Brown Lantern Donut House Anacortes Brewery
And some great sights: Cap Sante Washington Park Anacortes Community Forest lands and Mt Erie Rosario Beach * Deception Pass"