Love SFO - FYI on the Cali board there is a couple of good, recent SFO threads. With lots of suggestions
Columbus Ave from ChinaTown to the Wharf makes for a really interesting walk.
CityGuides offers tours of all the major attractions (free)
Exploratorium would be a must if my DD had any say
Alcatraz is really cool, especially the night tour but honestly I would not take small kids, I don't think they get it and that it is enjoyable for them.
We were in SFO in early March and there were about 10 sea lions hanging out at the pier.
A cable car ride is certainly a unique experience and one I would highly recommend. The Market/VanNess line is far less crowded and goes up over Nob Hill, past Grace Cathedal, the Fairmont and the Mark Hopkins hotels. You can catch the cable car at the south end of Grant or Stockton Street on the outskirts of China Town (near the main gate to CT). I prefer to wander Stockton as Grant is the tourist street and Stockton is the "locals" street. The food markets are something to see.
Ice Cream sundae in Ghiradelli is a "must do" for a tourist as is a walk out onto the Golden Gate Bridge.