I am from San Francisco and it is a beautifu place to dock because you are not far away from everything. Pier 39 is not too far from where the cruise ships dock and from the Ferry Building (Pier 1) it is just down from Market Street and off from Union Square where the shopping is. There are a lot to visit and remember if you want to go to Alcatraz, remember to make reservations. There are several boats such as Red & White Fleet, Blue and Gold Fleet. They leave from Pier 39.
I also suggest taking public transportation which is the MUNI. It is accessible to a lot of the tourist places. Remember also that Parking in San Francisco is DIFFICULT. Parking is basically limited to a lot of the hotels. There are parking fee and they are just way too high. You can forget about street parking too if you intend to drive in the City. They are strick and they are expensive.
For those wanting to stay in SF, it is rare to find something reasonable when it comes to hotel.
I have always suggested to stay at the Lombard Street / Marina District area. It is not far from Ghirardelli Square and Pier 39. From the Marina District, it is about 2 miles to the Pier from where the cruise ships leave but remember, you are talking about Hills, Hills, Hills,
For those of you flying early to SF, remember that the Airport is approximately 30 mts. away from downtown. The airport is actually situated within South San Francisco area.