Dang -- I just checked the website for the Bay Model and it looks like they're closed until the end of May.

For history, there used to be a walking tour of the area where they used to build ships. They would tell you all about the role of the shipyard in building and repairing ships during WWII, and how a lot of Rosie the Riveters worked there. The docents seem to be associated with the Model, and I imagine they must still be able to run tours even if the Model is not available for viewing. It's worth giving them a call:

http://www.spn.usace.army.mil/bmvc/b...ship_tour.html

There might also be some easy-to-access trails up to the Marin Headlands &/or the Golden Gate Bridge. Visitors center for the GG Bridge is on the SF side, don't know if you'll have time for that.

Also, I used to rent kayaks out of a place called Sea Trek. That section of the Bay is beautiful, calm, and a manageable size. They're not far off the main drag either.