So the kids want to go to San Francisco
I have a 6 year old daughter and a 5 month old son. We have lived in San Francisco for the last 8 years and it is great for kids. There are a number of kid friendly museums and a world class zoo for them. I'm going to discuss my daughter's two favorite museums in the city.
The first one is The Academy of Sciences at Golden Gate park. It may be hard to find, but it is well worth it. This is by far my daughters favorite museum. Why? There is so much for the kids to see and do. Walking through the circular tropical rain forest is a must. There are hundreds of colorful butterflies flying around and the animal and insect exhibits keep the kids fascinated. There is also an aquarium there. You have large tanks with sharks and a number of other under water creatures including a penguin exhibit. If your kids are between the ages of 4 and 12, I would definitely bring them here. Be aware of the price tag because it isn't cheap. Tickets are over $20 for each person entering, but it is well worth the price of admission.While you are there, consider eating at their cafe or restaurant. It is always run by an first rate chef. Currently, it is run by Charles Phan of the Slanted Door.
The next best place to go would be the Exploratorium at the Palace of Fine Arts in the Marina district. I would recommend this museum for ages 5 - 14. It is very hands on and it keeps the kids engaged throughout. Don't miss the exhibits on the second floor where the kids can play with sound exhibits. This museum is much more science intensive so the younger kids really won't appreciate everything that is going on. I would stay clear of the cafeteria at the Exploratorium unless you don't mind fast food. Not to my liking and I wouldn't let my daugher eat here.
If you're coming to San Francisco on a day trip with the family, both of these are perfect destinations.