I was happy to see the NY Times article on the ferries between the San Juan islands. I was over there this summer for a conference and a group from the conference took one of the ferries to Lopez island. It really was incredibly beautiful. The Times story online has one photo hinting at the kind of views you get, and there are a few more photos in the print version. If you’re anywhere near the San Juans, getting out to the islands is highly recommended.
A word of warning though: if you’re kayaking on the waters between the islands, and it looks like a ferry might be bearing down on you, it probably is a ferry bearing down on you and it will probably get to you quicker than you think. I managed to stay well out of ferry routes the short time I was out there, but friends who were a little more adventurous had some impressive horror stories to tell.