"The best view of them all is aboard the Skyfari Aerial Tram, but if you'd rather walk, be sure to catch the giant pandas, the polar bears, and the elephant odyssey," according to the magazine.
"If you go during summer, try visiting at night when live performers jam the streets, and you can watch the animals' nocturnal behavior."
The zoo recently began a phased opening of its $68 million Africa Rocks exhibit, which includes a penguin habitat, a boulder-strewn islands in grassland savanna, a glimpse of the rugged Ethiopian Highlands, a woodland, a Madagascar forest and a West African forest.
The penguin area is now open, with the others becoming operational in the near-future.
Also making the top five were the Indianapolis Zoo, Woodland Park Zoo in Seattle, St. Louis Zoo and Bronx Zoo.
The Living Desert in Palm Springs was sixth on the list, which was published last week. The magazine called it "undoubtedly the best desert-themed zoo in America."
Rounding out the top 10 were the Columbus Zoo in Ohio, Alaska Zoo in Anchorage, Henry Doorly Zoo and Aquarium in Omaha, and the Brookfield Zoo in Illinois.