I wrote this article last year - I suggest you check it out:
Cruisemates; San Diego Cruise Port - attractions in the most convenient asnd charming port in the U.S.
Web Sites to know
/ has an overview of almost everything you need to know about the interaction between cruise ships and San Diego. A very extensive site.
includes a listing of every cruise leaving from San Diego, parking lots with prices, outlines of local attractions, and much more.
has a listing of park-and-cruise hotels, which offer various packages if you stay at the hotel. Some offer free transportation between the airport and the cruise terminals. Other hotels allow you park your car in their lot for free if you stay at the hotel pre- or post-cruise.
San Diego Car Free
: An entire web site devoted to seeing all of San Diego county without a car. Complete instructions on how to get anywhere using public transportation.
Transportation in San Diego, California
: Airport, Amtrak, Car Rental, Trolleys and everything else you need to know about getting to and around San Diego.