If you go to the Bronx Zoo, also check out Tiger Mountain and the Butterfly Garden for the koi. Congo has some smaller tanks that are more specialized, including endangered cichlids from Lake Victoria and archerfish. There's also quite a colony of fish living in the alligator (or was it crocodile?) exhibit in Madagascar.
I haven't been to the NY Aquarium as a visitor since I was maybe six. I really need to find time to go