Hi K., when are you going? just wondering if its summer or winter. If its summer be sure to get some beachtime in when you are in San Diego. Lots of good beaches all with fun beachtown vibes.
I grew up in LA area but lived in San Diego for about 5 years after college. I would highly recommend the San Diego Zoo! A great zoo. It's pretty big, you'll be walking a lot. I recommend the beach more in San Diego. I like the northern beach towns- La Jolla, Del Mar, Encinitas. The gaslamp district (downtown) is nice to have dinner in one night and just walk around, if its baseball season and your kids like sports, consider squeezing in a Padres game, it's a pretty neat stadium and right downtown.
Disneyland, You could do it in one day if you plan to spend the whole day there and you pick a day that is not too crowded (not saturday and not a week when every single other person in the world is on a break from school). With two tween-age boys that could probably last from open to close, I think you can get it all in. You might want two days though if you want to do both parks (Disneyland and California Adventure). California Adventure would not be as long of a day as Disneyland. It's worth a visit though, it has some good rides and ambiance.
I would definitely skip whale watching. I have never seen any whales off the coast of california. I have been whale watching on a boat and it was terrible (cold, rocky, no whales, trapped for several hours). Honestly you might see more whales going up to the Point Loma lighthouse in San Diego (actually I think it might be called the Cabrillo Lighthouse, but it's in Point Loma), it's high up and great view of the coast and you ca occasionally see whales there (though I myself never have, not that I;ve been up there THAT much!)
I also don't think Sea World is that great, but I guess it is cool. There aren't many places to see giant marine animals in the world. If I had to pick between Sea World and the zoo, I would definitely pick the zoo! And I would pick the Zoo over Wild Animal Park. The WAP is more lazy, spread out, and the animals are further away (they are more in their natural habitat though). The zoo has more variety of animals. Side note, the food at both those places are pretty decent, and they sell beer throughout the parks ;)
Universal will not take you the whole day and I think it is also one to skip if you have to cut something (being that you went to the one in Fl).
I think the best park to hit up is Disney/Ca Adventure, I mean nobody does it like Disney. Then I'd spend a lot of time in San Diego!
And ditto LeeLee about the driving between Anaheim and San Diego. And don't plan to drive to San Diego on a Friday between 1pm and 7pm. Or drive back up to LA on a Sunday afternoon/eve.