Hi Jeff,
While the San Diego Balboa Park Zoo offers some nice shooting opportunities, especially from the top deck of the tour bus, I would highly recommend the Wild Animal Park. Take the train ride through the park a couple times and if you take along something like the 100-400 with a 1.4x tele or whatever the equivalent is with your camera, you can get some great shots. They also have a "photo safari" where they take several photographers in the back of a stake-bed truck and stop to let you shoot (mostly ungulates, & other browsing, non-predatory animals), I would not recommend it. It's dusty, dirty, bumpy and you can do as well or better from the monorail train which doesn't cost an arm and a leg.
Lin