Have you checked out Alt School in SF?
https://www.altschool.com
and the new Stratford in SF
http://www.stratfordschools.com/San_Francisco_Preschool_Elementary_Middle_School
Personally, I have not used these 2 schools, but you could attend their open houses to see if they interest you. There is a new Alt school coming soon nearer to me and I might visit them at that time.
How far south are you able to commute daily for school?

I have been in your shoes (a little south of you) and what I did was to put my son in the best school situations that I could find while after schooling him extensively to challenge him and biding my time until I could find a better fit for him. We have changed 3 schools so far and are changing to the 4th one next year (he is a 2nd grader!). Good luck.