The Safari Park is part of the San Diego Zoo system. They also have a conservatory. It is easily the best zoo I've been to, but expensive. Also, watch out for staff really trying to pressure you into becoming a member.
Sea World is controversial. I never had time to visit it when I was there, but I was half tempted to just to spite PETA, even if the park is pretty much infamous for poor/cruel treatment of its animals.
If your family likes baseball, Petco Park is a great place to watch a game.
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