The Bay Area Discovery museum is a neat place to take children. It is like a minature of the Exploratorium, where children can touch, play with, and particpate in most of the exhibits. The museum is composed of several small buildings that contain the exhibits, and there is also a small playground in the middle. The musuem is located almost right on the water, with the Golden Gate Bridge in view.
Definitely a must-see for families with children. You may want to bring your own lunch though, I don't remember there being a snack bar, although it may have just been closed when we went. Call to make sure.