Hi, Good for you for planning ahead for your summer vacation!

When my brother took his wife and two young kids on a road trip across the United States a few years ago, their first destination was San Francisco. They drove up from Southern California, and stayed at a hotel near Pier 39. While they really enjoyed the many entertainment options at Pier 39, including the Aquarium of the Bay (http://www.aquariumofthebay.org/ ), the feedback he shared with me was that there was a lot of traffic along the Embarcadero, and he would probably have his family stay outside the city next time and take the BART subway into the city to go to museums and other tourist attractions. Other feedback: it can be cold and windy in San Francisco during the summer, so dress in layers.

You didn't mention if your family was traveling by car or plane, but either way, you may find these resources helpful for keeping the kids happy (and their minds active) on the way: http://www.education.com/special-edition/family-road-trips/

One article in that info center, "Kid-Friendly California Fun and Learning", includes several educational tourist activities in San Francisco: http://www.education.com/magazine/article/California/

If your kids are young (under five), there's a place across the bay in Berkeley (that you can get to really easily via BART - downtown Berkeley stop) that I highly recommend. It's a play-based learning museum called Habitot Children's Museum: http://www.habitot.org/index2.htm  
Our daughter's favorite activities at Habitot were making art on the painting wall in the art room, and getting wet at the water play stations in the back (she also enjoyed a wind and kite display they had when we went). It's very affordable and truly enjoyable.

Have a great vacation!