Proof School is a grade 6-12 independent school in San Francisco, offering a transformative liberal arts education for kids who love math.
I suggest checking out The Academy in Berkeley and if your son really likes math the Proof School in San Francisco. I have children at both schools. The Academy is a small school, but very academically oriented. I feel my child is getting an excellent education there. Proof School is also excellent school with a math emphasis....They also have strong science and computer science classes. Many kids at Proof School live in Berkeley and commute on BART. If your son really enjoys math, I would suggest visiting. I've also heard good things about Black Pine Circle.
This wonderful school does itself a disservice by the tagline: for kids who love math. It is true that the school has an emphasis on mathematical competence, and if you have a "pure math" kid, it is essentially your only choice - not just in the Bay Area, but anywhere in the US as far as I am aware. It is also true, however, that the true orientation of the school is simply toward kids who love to learn. My son, for example, loves history much more than math, and would not want to go to any other school. Anywhere. Period.