If you told me a few months ago that I could do a fun big city vacation with two little kids, I would have thought you were nuts. But San Francisco is an awesome city, even for little kids! I'm going to tell you what we enjoyed the most, so if you are planning a trip to SF with your kiddos, you should check out these spots!
Bonus - you drive over the Golden Gate Bridge!
Ghiradelli Square - Take the cable car down to Ghiradelli Square, and enjoy a large open park by the bay. Lots of shady trees and green space to run, and you can enjoy ice cream and chocolate from the Ghiradelli Ice Cream Shop. Also explore the chocolate store, and your kids can see big vats of chocolate being churned.
The cable cars are a fun ride, and you see so much of the city, going up and down the steep hills of SF. Beware there may be a lengthy wait for them in the sun. Make sure and wear hats to keep heads cool while you wait in the sun.
Bonus - If you pick up the cable car where it turns around (downtown and in Ghiradelli Square), it is very cool to see how they manually turn the cars around!
Aquarium of the Bay - A small, multi-level aquarium on Fisherman's Wharf, I found it a little pricey, but I did get a good discount on tickets by searching online. It has tanks filled with different sea creatures and fish, an area where you can touch some of the them (like rays and starfish), and the best part of all, a tunnel you can walk or glide through (on a moving ramp) and see all the fish around you and above you swimming around.
Bonus - It's not a huge place and will probably take you about an hour to go through. So by the time the kids start to get cranky, you've seen everything anyway!
Did I mention it is also a winery? Yes, fun for everyone! :) Their wines are amazing, and the general admission price gets you a tasting of five of their wines. Note - there is also a Family Room where you can taste, it is a larger room with a table with crayons and paper so your kids can sit and color while you taste. When we were there, it wasn't very crowded, as the adults without kids were in other tasting rooms.
Bonus - there is also a ton of farm animals outside in a pasture that your kids will love to see - chickens, sheep, even an emu!