There's few places along the shores of San Francisco Bay where you can camp. Angel Island is the one public campground that is right smack in the middle of the bay.
Each of the bay area cities and counties, including San Francisco, Alameda, Contra Costa, and Marin, provides a wealth of information on their web sites.
An assortment of links to useful articles and resource sites for visitors to San Francisco.
Schedules and routes for ferries, buses, and other public transit in the San Francisco Bay Area.