There is long term parking across the street from the cruise terminal. It cost us $10.00 per night and is secure, not sure of the name, but it was reccommended by our cruiseline (Celebrity). It is convenient because you can drop off your luggage at the terminal and walk back about 100-200 yards. We will be using it again this May for another 14 night cruise.
On our last cruise out of San Diego, that parking lot was under new ownership (or management ?). It was $12.00 a day and we were on a 7 day cruise and they charged us for the 8th day. It also had to be paid by credit card ONLY. What a rip off, but it seems that they are the only game in town.