I, too, would recommend Sea World, although I won't go because the whole Whale in a cage thing bothers me. It has a kid's play area that has areas geared to the little ones. The shows are fun and there is complimentary beer tasting in the hospitallity center!!
The zoo is awesome and unbelievable and not to be missed...but a three year old will run out of steam pretty quickly. So, if the trip is to keep the 3 year old happy, Sea world, if not quite as important, the Zoo. It would be a crime to come to San Diego and not see the zoo.
Another poster suggested the "Wild Animal Park". Again, not to be missed as an adult, or older kid...a three year old will like the Merry-go-round...actually I think it is officially a Carousel and the Lorikeet landing, but my daughter who is now 6 has just recently liked the tram ride and she is an animal enthusiast. So FANTASTIC...but your youngster might be a bit fussy!