If you have small children flying with you, I would try to avoid flying OUT of San Diego. The security area is the worst for getting everything back together when you're trying to corral your kid(s). The area is tiny and if you lean over to tie your shoes, you block most people behind you, and last I went there were only three chairs to sit on. And the security line rivals the Space Mountain queue in the summer, going back and forth and back and forth.
I love visiting my brother in SD, but I hate flying home from there!
I will mention that I fly Southwest so there might be other security lines for those traveling on other airlines, I don't know.
I have flow into Ontario and SNA. ONT was cheaper, but getting to DLR was very expensive via Super Shuttle. SNA was more expensive in general, but super shuttle was a quarter the cost as from ONT. In addition, the Grayline Anaheim
Disneyland Express bus was available from SNA (and LAX) but not from ONT.
Will you be renting a car? If so, be sure to check that you can rent in Anaheim and drop off in SD, and make sure the price is OK for you. If you don't want to rent in Anaheim, I've been intrigued by the SurfLiner train from Anaheim to San Diego. I figure you could take a taxi from the train station to the hotel, or get a rental around there... We always have my brother as our little SD shuttle service, so I don't know much about getting around SD, sorry!
I hope others have more info for you!