When I went up last year, It was cheaper to take the car over to an island on the ferry (with 2 people in the car and 2 bikes on the back), rather than pay to park in the official lots. There is a surcharge for tall loads, so beware of bikes on roof racks which would bump you up to the higher cost. Inter-island travel is free as I recall, both on bike or car, once you pay for your initial trip. But you won't have to wait in a long line if you're on a bike!
There was another thread on here earlier this summer about biking the San Juan Islands. Had some good info...