You can use Craig's List to find individuals renting out their spots. If you want a controlled-access garage it could cost $275-$350/month. The Mission Barlett garage charges $220/mo. for all times access, and slightly less for daytime only monthly parking.
As a permanent resident you can get an annual parking permit for the zone where your home is located for $109/year, or $54 if it expires within 6 months. The San Francisco Metropolitan Transportation agency issues permits that expire different times of the year depending on your zone. You'll need to go to their offices with a completed application and proof of residency (see their web site for more information).