There is a large parking lot directly across the street from the cruise terminal in San Diego. It is outdoor parking and I am not sure of the charge per day. Probably find it on the net.
My 2 trips into SD with car, I chose Holiday Inn and Holiday Inn Express that had a stay, park and cruise program. I stayed a night before, first night car park was charged $12, then the week was charged at $7 a night and it was an underground garage. The Holiday Inn lot is roomier for larger cars. Free shuttle to (and from, if you call them when you get back) the terminal, a short ride away from both city properties.(I cabbed back to my car each time as not to waste time).
Much more reasonable that the Holiday Inn Bayside! (which is across from the cruise terminal, and other good stuff).
Hope that helps a bit.
There is also a multitude of airport parking nearby and you can cab over. Again, not too far.