We travel to the San Juans several times a year (just by car, no trailer) and as far as I know, the only ferries to the San Juans originate in Anacortes. Fares have gone WAY up in the past few years, and the number of sailings have been reduced. Also, you need to make a reservation for the sailing you want, and unless it's on a weekday at an unpopular time, you'll need to do that several days in advance. And, at the current time, they're a boat down, so the schedule is completely messed up.
https://secureapps.wsdot.wa.gov/Ferr...e/default.aspx