Check out Nob Hill Motor Inn. They have a family room, their rooms are very clean and large. They are also in a safe neighborhood and within walking distance to everything and lots of great restaurants. I personally would avoid staying near union square with kids, many homeless and crack addicts, no problems shopping the area, lots of interesting characters in the evenings though. Buy the muni passes, you can ride the buses, cable cars and trolly all you want. When we return to San Fran we will be staying at the Nob Hill Motor Inn with my family, My kids are 11, 13, 15.