a taxi to the downtown area of SF should run around $25-30 and since there are so few cruises that leave from there, that is what I would do.
there are also van transfers available to the downtown hotels so I don't see why they couldn't take you to the dock as well. They are cheaper but you have to arrange in advance for quicker service. A taxi is there waiting for you ready to go.
This probably isn't for everyone, but starting June 22nd the Bay Area Rapid Transit (BART) system will be offering service from the airport to downtown (Market and Embarcadero). The BART station connects with light rail that takes you the last mile right to the passenger terminals. If you are travelling light enough to carry your own bags, the total fare would be about $5/person.