I'd suggest a cruise on the Bay. Goldstar frequently has the "Bridge to Bridge" cruise on discount (Red and White fleet) and it is a lovely and scenic ride. Today, I was on a (no) whale watching boat ride on the Bay and out a bit past the Golden Gate. No whales decided to show themselves - just a porpoise and some sea lions, and many many pelicans and ducks and other marine birds. There were a number of kids on the boat, including a school group (10 years old or so), enjoying themselves.

Parking? See if your rental permits a car dump off somewhere central in SF, and then don't have a car in the City. Hotel parking is now in the $70+ range at the downtown majors.