While not a brewery Hi-Times Wine cellars in Costa Mesa is awesome. Doubly so if you are into wines as well as beer.
In the San Diego area you have a ton of options.
Belgians? Pizza Port brewing. I usually go to the San Clemente shop.
http://www.pizzaport.com/ (the san clemente location is more pizza place and also has a lot of good guest taps and one beer engine)
Stone brewing is awesome and a very good tour as well.
http://www.stonebrew.com/Also in San Diego is Ballast Point, I haven't been there is a few years, when I was last in it looked more like a LHBS with a tasting bar than an actual brewery but the beers are very good
http://www.ballastpoint.com/Green Flash, like stone, is one of the real hot beds of "west coast" style IPA. I haven't visited their brewery though. It's in Vista.
http://www.greenflashbrew.comAnd of course, you gotta pimp Mofasa's place. The BJ's in Laguna Beach is pretty nice. In Laguna there is also Ocean Avenue Brewery, really a brewpub and not overly exciting. I wouldn't go out of my way but if you're in LB anyway might stop and get a pint.
ETA: Sorry about that. I somehow read the earlier post to say that YOU were planning on driving from LA to SD on the trip. I don't know anything at all about Palmdale.
