Love San Francisco

Check out the City Pass and see if you can get your money's worth out of it. We found it worthwhile but YMMV
Golden Gate Park is very nice and the Academy of Science would be good for your ages. Took the bus there from the Fisherman's Wharf area, enjoyed the ride through Haight-Ashbury , Also enjoyed the Exploritorium, your 14 yo is on the upper age for it but will be ok if she has some interest in science stuff (my son was 14 and was fine with it).
Take one of the boat trips on the Bay that go under the Golden Gate (that was part of the City Pass). Just remember that anytime you're out on the water it's going to be windy and chilly... layer up for sure.
If you're there on a Saturday morning,
check out the farmer's market in the Ferry Building. The building itself is worth seeing and the market is AMAZING! Really envy people who can shop there every week.
We stayed in the Fisherman's wharf area without a car - it's more hassle and $$ than it's worth - and did everything we wanted to in the area using public transportation (again part of the City Pass). Then grabbed a car, hit the Exploritorium on the way out of town (not as easy to get to on the bus) and stopped at Muir Woods. After that spent several days in Point Reyes/Half Moon Bay/Sonoma before driving back to the airport. Worked well for us and kept our costs down.
The highlight of the trip was a Segway tour. My son still talks about it 4 years later! Minimum age for it in SF is 14, may not work for your family. But if you're looking for something to do just with your older child I can't recommend this enough!
Have fun!