[Ponine]

GD's pretty spot on.
I live in La Mesa, and on a good day I can make it to DLR in 90 minutes leaving fairly early, and driving quickly.
Two hours is a safe bet, barring accidents and rush hour traffic.

I've never had issues on the drive home at all. It's always been on the way up.
If you'll be doing the sightseeing thing, look into the City pass, I dont know the pricing, but i've seen it at Costco, and DLR. Seems that in a 14 day period you pay one price and get into DLR, the SD ZOO, the SD Wild AP, Sea world... Darkbeer might know specifics on that.

How old is your son? Mine's 6 1/2.
We've also got a funky little nature preserve down south of us, with a manta ray pool; lots of things to see in Balboa park. Jot me a pm.. we'll compare notes.
You will spend an entire day at any of the three major sd attractions easy. Old town would make for a whole other day on top of that... I'm rambling... just holler.