I only have 10 years SV on my back, but here are some points I have observed. SF as mentioned is not a place you want to have your children to go public school. I was told that schooling is not necessarily assigned to your local area and you can end up sending your child to school by bus, which I think is not such a good idea.
My home is in Redwood Shores and Peninsula overall is a good place to be (except East Palo Alto) with children, many good schools. Most cities on the west side along the foot of the Mountains are prime locations like Los Altos, Saratoga, Los Gatos, Woodside, but for sure not cheap. There are a couple of cities very desirable for families, because of the good schooling like Cupertino, Fremont Mission, Foster City.
You will find many good places to raise your children, but for SV has a steep price tag. Personally despite living at a nice with highly rated schools I still ended up enrolling my daughters into private school, which tells a lot about California and the broken education system. Good Luck