First of all, in my opinion, no one in their right mind would ever visit Las Vegas. I lived there four months (against my better judgement - long story) and it has zero redeeming qualities and is also the only large U.S. city with no real zoo. (The one so-called zoo they do have, Southern Nevada Zoo, is a tiny roadside disgrace).
New York City - Bronx Zoo is a must, as others have said, and the same group that runs it also runs three smaller zoos and the aquarium. I think at least Central Park Zoo would be worthwhile if you have the time (new snow leopard exhibit).
Washington DC - National Zoo of course. Baltimore (Maryland) is nearby and has a decent zoo as well as the National Aquarium. Philadelphia Zoo is 100 miles away by train (I think) and has some good stuff, especially Big Cat Falls and Giant Otters.
San Francisco - Have not been to either zoo there, but from everything I have heard Oakland Zoo is better than San Francisco Zoo. If you want to try an animal theme park, Six Flags is just north of there and has the famous diving tiger show.
Los Angeles - The other posters on this thread have nailed it - outstanding collection in average exhibits. Greatest strength is primate collection, so if you are monkey fans it is a must. If you are cat fans, the Exotic Feline Breeding Compound is an hour and a half north by car. Small compound, lackluster exhibits, but perhaps the best cat collection in the country. Aquarium Of The Pacific in Long Beach is also quite good.
San Diego - Again like others said, both the zoo and the safari park (formerly Wild Animal Park) are musts. Be sure to allow a full day for each one - get there when they open and stay until they close. Whichever one you go to first, you can buy a two park pass to get into the other one (these zoos are not cheap). If you are wolf fans, there is a wolf center in some scenic foothills just east of the safari park. (Never been there myself, but it looks kind of cool. I forget the name, but a Google search should turn it up).
If you want to take a day trip to Palm Springs, which is two hours north of San Diego or two hours east of Los Angeles, The Living Desert is one of my favorites (partly because of the outstanding wild cat and wild dog collection). Focuses on desert animals exclusively. And if you are elephant fanatics, I would invite you to come on over to Tucson, which is a cheap one hour flight on Southwest Airlines from either Los Angeles or San Diego (or a six hour drive east from San Diego). Reid Park Zoo's new exhibit, Expedition Tanzania, will be open by then and should be one of the top elephant exhibits in the country - probably top three. Of course Tucson is also home to the very highly rated Arizona-Sonora Desert Museum. (Search ZooChat and you will find nothing but praise for this institution).
) haah, asian complex with giant pandas. Have Fun 