I Know Why the Caged Bird Sings by Maya Angelou
Autobiographical. Part of it takes place in Washington High School.

The Basic Eight by Daniel Handler
Not strictly a San Francisco-based novel, but it has many parallels with the Lowell High School of San Francisco (Handler's alma mater). Lowell students and Lowell alumni will find this especially interesting. See if you can spot your teachers!

The Joy Luck Club by Amy Tan
It "intertwines the lives and generations of four immigrant families to San Francisco and shed light on the multi-faceted relationships between mother and daughter."

A Hearbreaking Work of Staggering Genius by Dave Eggers