There's Foundation Directory Online [1]. It's super-expensive, but you can use it for free at a lot of libraries, including in San Francisco. The group that runs it, the Foundation Center, also runs seminars on how to run a non-profit and raise funds, and they have a branch in SF too.
Instrumentl is used pretty heavily by nonprofits, however nonprofits working in the fields of science education and environment (at the moment). What fields are you working in?