A couple of suggestions - San Fran is great and lots of fun things to do there. We went sailing in the Bay last year (pricey) but the kids are still talking about it 18 months later. Our instructor let the kids guide the sailboat under the Golden Gate bridge and back. We were cold, wet and the boat was sideways most of the time but will definitely do this again!
If you have time to get up to Napa or Sonoma counties, I'd recommend a winery tour that focuses on growing, production and the 'chemistry' behind making a bottle of wine. We did Ferrari-Carano (
http://www.ferrari-carano.com/) and the kids had a great time. They really focused on the geography of the area, machinery behind the business and the trees that produce cork for the bottles. Plus the gardens are just amazing and a real treat to walk through.
Muir Woods is a great park to walk through and is very close to the Golden Gate Bridge.