I can't imagine not going to Disneyland with a 6 year old.
I think you should go to the Aquarium of the Pacific in Long Beach--it is an amazing aquarium for all ages & he will get to pet a shark! If he is into ships you could go to the Queen Mary which is right there too. Also, he is the perfect age for Legoland which I think is one of the nicest theme parks out there for kids. I guess you could take a train there--it's kind of halfway between LA and San Diego.