The Hotel Parking lot, I can't remember the name. Check them out anyway, they might let you. The public lots a scary to me but someone might know a good one.

I think the Embarcadero garages are good places, but you have to get there really early in the a.m. Another moto-friendly garage is the City-owned one up on Bush St., just below Stockton and above Grant. I think another is the Crocker Galleria, on Sutter, just below Kearny. Most private garages tend to refuse motos. Have read on BARF recently that moto street parking has opened up, like along Sansome (near Market). Best to check on SF's parking web page, because some months back moto parking costs rose sharply (and the tickets for expired meters are high too). Some meters require prepaid cards. Don't forget a good wheel lock and to remember it's there before you ride off.