This is a poor-man's luxury scenic cruise to be sure. For details on the San Juans, one of the West's most wonderful tourism and cruising areas, please see my journal on the Islands. Here, we're just dealing with transportation issues.
Generally speaking, people get to the San Juans by Washington State Ferries leaving from the docks in Anacortes, several hours north of Seattle and not a very convenient place to try to get to on bus or thumb. But there are alternatives which we will get to. If you are driving, note that there are no reservations and in summer and big weekends there are LONG lines, so get there early. Or leave the car in Anacortes. The ferries stop at Shaw, Lopez, San Juan and Orcas islands, then continue (if you wish) to Sidney, British Columbia, where you can get transportation to Victoria if you wish. Ferries charge only outbound from Anacortes, coming back is free. Maximum fare for the Island Passage is $5.10 for walk-ons $22 for car & driver. Whale-watching, seal-spotting, and scenery-gawking is free.
BUT, the Victoria Clipper operates service to San Juan Island directly from Seattle, and once there, you can island-hop on the cheaper State system boats. Fares from Seattle to Friday Harbor on San Juan start at $49.
Another little-known lick for carless travelers: there is a private passenger ferry called P.S. Express (360385-5288 in Port Townsend) that operates between Friday Harbor and Port Townsend, the beautiful gingerbread Victorian town on the Olympic Peninsula (please see my Olympics Journal). Pricey at $49 a head, but a way cool trip, very likely to spot sea otters, orcas, sea lions.
So, you don't need a car to do the jewels of Puget Sounds. Seattle to Friday by Clipper, Port Townsend by P.S. Express. Or Seattle to Victoria, then Port Angeles by private Ferry, back to Victoria, and on to the San Juans.