I would stay at the Marriott Downtown. They have a pretty decent breakfast buffet.

There is a museum one street over from the hotel and Yerba Gardens (I think I got that right), as well as a movie theatre with a food court. In the movie theatre there was a child interactive project based on a children's book (the name escapes me with now). When I took my brother to SFO, we stayed at the Marriott and we went to the movie theatre for downtime.

Plus the cable car ride from downtown to the wharf is awesome going down the hill.

With children I would stay there before I would stay at either one of the Renaissances' or the Wharf.