The big employers I know are SAIC, UCSD, and Qualcomm. I believe they are the 3 biggest.
If I have time, I’ll research this. I want to because I had to laugh out loud last week when someone wrote that people would be able to handle their ARM adjustments because they would get big increases in pay. San Diego has notoriously had no businesses headquartered here (and thus very few high-paying jobs), and is extremely low on the salary scale to begin with.