Another NYC zoo backed by the Wildlife Conservation Society, Queens Zoo is always a nice addition to any itinerary in the area. First established in 1968 on the site of the Flushing Meadows World's Fair, this zoo is probably most well-known for one major thing: their aviary!
The aviary onsite uses the geodesic dome from the worlds fair and provides a seriously impressive bird habitat. Outside of the aviary, your group can also explore the Animal Trail (bison, deer, etc), Domestic Animal Zone (Texas longhorns, Canadian Lynx, etc), Sea Lion Pool, and Waterfowl Marsh. There are various Conservation Stations throughout the zoo to visit, a small Cafe Shop onsite, and the opportunity to see sea lion feedings daily.
While in NYC you may also want to check out the Bronx Zoo, Central Park Zoo, Prospect Zoo, or NY Aquarium.