I have actually seen all three (Audubon, Jax, Palm Beach). However, they will all be out done when Miami and Los Angeles open their neotropical exhibits.
Audubon's Jaguar Jungle has a small collection (Jaguar, Anteater, Spider Mnky). However, the exhibit is laid out well, the enclosures are well built, and the immersion is excellent.
Jax's Range of the Jaguar has an awesome collection (Jaguar, Harpy, Giant Otter, large Aviary, Tapir, Anteater, various monkeys, and a very diverse and large reptile collection including a caiman lizard). There is no laid out path to follow, the exhibit is more of a plaza with the exhibits surrounding it. The Jaguar enclosure, Aviary, and Reptile House are superb. However the remaining exhibits (Otter, Harpy, Tapir, Anteater) dont quite compare to the other enclosures. As of now this is the large Neotropical exhibit in the country.
Palm Beach Zoo (whose exhibit was designed by Torre, who also designed Audubon) is the better themed of the three with several Mayan temples, a latin marketplace, and various other features. A good collection (Jaguar, Capybara, Bush Dog, Tapir, Rhea, Anteater, various monkeys, caiman, and various small mammal/reptile species) fills the enclosures. However the exhibit is unfinished with a phase II in design (to include and huge aviary, giant otters, large freshwater tank, and a slew of more cool animals). When finished, it will out do all neotropical exhibits that currently exist.
And lets not forget the other neotropical exhibits:
San Francisco
Santa Ana (the whole zoo is neotropical themed, or will be)
Phoenix
Buffalo
Mesker Park Zoo (newly built)
Sedgwick County Zoo
Brevard Zoo
Topeka Zoo
Dallas World Aquarium
Toronto Zoo
Others planned or in construction:
Miami Metrozoo
Los Angeles Zoo
Beardsley Zoo
Nashville Zoo
Elmwood Park Zoo