I can't help you much with the boat charter, unless you are looking for a 500' training ship...but as far as fun stuff to do:
Alcatraz Island (tickets sell out a few weeks in advance)
Giants will be in town
Point Reyes national seashore (I am going camping there this weekend, absolutely beautiful)
Napa and surrounding wine country, I suggest the Rutherford grill for dinner
SS Jeremiah O'Brien and the USS Pampanito are docked at Pier 45, fun little tour
Just a few ideas, if you tell me more what you are looking for I might be able to help you out some more. Other than that, if you are cruising outside the gate beware of the potato patch!
Dan
Oh, and dont forget In-N-Out
