It also has a great aquarium - the only rival is the spectacular one in Monterey. Right across the way is the modern art museum the De Young. There's a tower with an observation floor - on a good day, the view is great. Not many people know it's free, and you don't have to have a museum ticket. Also, paddle boarding around Stow Lake is really great on a nice day.
If you are going to do a ferry, I would probably suggest the one back/forth to Sausalito or Tiburon (and not Jack London), as you can almost count on better weather.
In the Presidio, the newly renovated officer's club has a nice review of early SF history and military tradition. Admission is free. Nearby is the Disney Family Museum. I have not been as I've heard mixed thing about it (particularly for kids). There's a lot of early drawings from cartoons which are probably more interesting for adults than kids. Again, haven't been.
But a walk along Crissy Field, lunch or snacks at the Warming Hut is a good day. Early October could be absolutely glorious with weather. Continuing on to Fort Point and climbing to the very top - the GG Bridge is so close you feel you can touch it. Just walking across (or to mid way) on the GG Bridge is a treat.
The Exploratorium is hands-on science-y stuff. If she's into it, it's a fun time for sure.
Aquarium of the Bay is just ok - the one in Cal Academy is far better, but if are there and can only do one it's not bad.
The SF Zoo is also just ok as once you get past the new spectacular African section it's pretty old-school depressing. The Oakland Zoo is far, far better, but it's probably too far.
If you have a car, driving up the Headlands immediately after crossing the bridge to Hawk Hill is great. Descending down, the backside is one of my favorite areas. Short walk to the Point Bonita Lighthouse, Playing at Rodeo Beach, The Nike Missile Site (now open Fridays and Saturdays), Battery Townsley (first Sunday of the month, 12-4).