San Diego is amazing. I love living here. I would highly encourage you to try and do Sea World and the Zoo.
Legoland depends on the ages of your kids, as I think it highly overpriced ($62 for an adult

) and not very much to do. Most days it is only open from 10am-5pm. Again, if this is a once in a lifetime thing, I would skip Legoland to do more Disney, or Sea World, or just a day at the beach in La Jolla or Carlsbad!
I would also split stay the two areas. You will spend far less time driving, and traffic is a killer.
EDIT: After reading the ages of your kids, they would probably love Legoland. Be aware that Legoland has very strict height rules on their rides, and can be hard on families with more than one small child.