If you don't mind driving into the city or taking the BART, stay closer to SFO and out of the city proper. Embassy Suites and so forth are in the Burlingame area and have parking.
This is probably not what you had in mind. I often stay at a Comfort Suites on Airport Blvd because it's cheap and room XXX (that I request) is very quiet. But it's nothing like the experience of staying downtown [I guess, never stayed downtown myself, mostly lived and worked in the South Bay].