Oh, here's another great idea if you have more days - rent kayaks at Aqua Verde near the UW campus a

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I've yet to figure the connections on the way back to Seattle, but unless Kitsap Transit has a direct run between Winslow and Port Townsend that is less than obvious on their web site, getting up for the very early ferry is the only way to make the connection and have the day to spend in PT.
Still not convinced it's worth the trip time unless someone can argue that Port Townsend is that much more fun than other options. (One day, we're taking the water taxi to Alki Beach for biking, seafood, and bumming.)
just to clarify, there was a temporary direct passenger only ferry between seattle and port townsend a couple years ago when the car ferry from port townsend to keystone choicehotels broke down. once a replacement ferry was put on that route, the temporary service was stopped. it was not a regular thing and it wasn't cut due to the economy in other words.
It was at the suggestion of a friend. Here we are on our second day in Seattle and have scuttled the PT plan. May have included it if the temp. ferry was still running. Replacing that idea with the water taxi to Alki beach tomorrow, renting bikes. Having a blast!
Super! Lucky you! Great weather. You'll love bicycling at Alki. Ask about the routes all the way to Lincoln Park. See if you can get a map. You can continue after Alki on the roads near the water. You go near a Coast Guard station and continue on. When the road goes up a hill on the left, you go straight on the little lane ahead, with houses on the water side and a park on the left. This short lane leads to the path at Lincoln Park (not paved). This area is like the islands. You can ride on this path to the Coleman pool in Lincoln park (salt water Olympic size public pool) and beyond on a paved path to the beach, with lots of driftwood and on to the Fauntleroy Ferry. It's a great ride and mostly flat.
Another interesting detour before you get to Alki is a small park off to the water side that overlooks the port. It's right there but a bit hard to find. It's close to where you will rent the bikes. It has great views. You can ride (or walk) your bikes to the viewpoints.
Oh, here's another great idea if you have more days - rent kayaks at Aqua Verde near the UW campus and visit the houseboats by kayak (Sleepless in Seattle, and all that). It's a wonderful way to enjoy Seattle. The Aqua Verde cafe has great food, so you can eat there when you return.