I live in SF but don't know of any hotels that offer transportation to the pier (usually ships leave from Pier 35). There aren'st nearly as many ships sailing from SF as there should be, though there are more scheduled for 2002 than in previous years due to the repositioning of more ships doing the Alaska itinerary.
That said, Pier 39 (practically next door) is a major tourist attraction with several good hotels and a cab would run less than $10, but remember that San Francisco encompasses all of seven square miles - no place is very from from any other place around here!
Let me know if you need a hotel hook up. I would offer a place too for the weekend or a few days for $40 night. Drop me a line. Cab far would be $10 to the Pier from mid-SF and all points closer to Piers. Bus lines by me all go downtown and to Piers too.