This website gives you a couple options. Also, there are four hotels in San Francisco that have Stay&Parks. Comfort Suites on East Grand Ave, Double Tree on Airport Blvd, Good Nite Inn on Airport Blvd, and Radisson on Sierra Point. You could stay at one of these hotels the night before your cruise and for the cost of your stay you can leave your car for up to two weeks. They will shuttle you to the airport. From the airport you could then get taxi to the port.