We were there over spring break with our 7 year old. Here were my favorite things:
1. Visiting the Walt Disney Family museum. Showcases Walt's life and his incredible contributions. This is stellar:
http://www.waltdisney.org/
2. Riding bikes across the golden gate bridge and then down into Sausalito. Have pizza and pastries in Sausalito on the waterfront and then ride the ferry back to downtown. I was worried about this (I had my 7 year old on the tag-along). But it was fabulous!!
3. Exploratorium. This is definitely educational, busy, and super fun. This is the best hands-on science museum I've ever scene:
http://www.exploratorium.edu/. Be prepared for a busy day.
Other times we've gone we've visited
1. Golden Gate Park. There are lots of things to do there. With family the Academy of Sciences is excellent (complete with aquarium)
http://www.calacademy.org/, but my personal favorite was strolling through the Japanese Gardens and having tea/snacks in their little café. If I didn't have my kids, I would also consider going to the art museum there. There is an amazing outdoor playground there too so that kiddos can run off steam. Here's the link to the park itself.
http://www.golden-gate-park.com/ Walking around the *green* park is also a nice change from the big city vibe.
2. Alcatraz - One of my friends said it can be difficult to get Alcatraz tickets unless you book way in advance. If you really think that would be fun I would call now. I personally would not do this with my 7 year old.
3. Cable Car Museum - ride the cable cars and then get off and visit this museum. It's free and small, but you get to see the actual cable that pulls the cars. Totally educational and awesomely geeky mechanical stuff.
http://cablecarmuseum.org/
Have lots of fun!!! I'll post again if I remember other things to do...