You can park in SAN Park Harbor Drive which has 800 long-term parking spots available. The cost is $16 a day, and it's located on Harbor Drive. Once you park and get your ticket, a shuttle will take you to the terminal.
SAN Park NTC is a larger lot, slightly farther from the terminal. As of October 2010, parking there costs $16 a day, and a shuttle will take you to the terminal once you've parked. You pay on the way out. It's located on McCain Road.
SAN Park Pacific Highway is the farthest from the terminal, but also the cheapest, with a price of just $10 a day as of October 2010. It holds 1,300 cars. A shuttle will take you to the terminal after you've parked. It's on the Pacific Highway.
Third-party lots are another option. Park 'N Fly and Park and Ride on Kettner Boulevard offer 24-hour service. Their pricing changes depending on days of the week and length of stay.