From the places I've been to, the two best by far are both in New Jersey (not too far from NYC though) - Absolutely Fish and Pet Shanty (spelling?).
The best fish selection in the city I've seen was in New World Aquarium, followed by Pacific Aquarium & Pet.
As far as Brooklyn, Brooklyn Zoo & Aquarium is the best I've been to. Not as good selection as above mentioned stores, but better then all other Brooklyn based stores.
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