Try the following link about San Geronimo Valley in Marin

I did a search for spawning salmon in San Francisco and came up with the following link. The article came out in Dec of 2005 so I would think the salmon run would be in December. Do a search for San Geronimo Valley may point you to the right direction.
http://www.sfgate.com/cgi-bin/article.cgi?f=/c/a/2005/12/25/BAGF6GDAE61.DTL&type=printable

If you don't find them in wild rivers, hatcheries would be the next best place to see them, not exactly the same as natural habitat but better than nothing.

Good luck with your search for wild salmon.

Haven't seen it myself in Bay Area. In Pacific Northwest, given the right time of the year, they are all over and sometimes people's backyard creeks.

Sometimes fishmen on Northwest docks will give away their fresh catch of the day, although I personally don't care for the taste of fresh salmon :-( (Smoked tastes better to me)