New World Aquarium is a nice place, good quality, sometimes oddballs, little pricey, but very knowledgeable staff.
In Chinatown: small stores, but good prices
Pacific Aquarium on Delancey
Win on Mott Street
Aqua Star on Mulberry Street
In Queens:
Fish Town, corner of Northern Blvd and Francis Lewis Blvd
Northern Aquarium on Northern Blvd, 1 block west of Main Street
Tropical Island Aquarium on Main Street, about 6 blocks south of the Main Street subway station (last stop of the 7)
Cameo on Jamaica Ave