In Nassau,
i have found 2 decent places specializing in just fish, used to be called Aquarium Adventure, now called Pets-warehouse, 177 Glen Cove Road, Carle Place, NY . Large selection of fish, many tanks, good to average prices on fish and supplies too, the old place used to have crazy high prices.
Also another place with a big selection, Tropical Showcase, 372 West Old Country Road, Hicksville, NY...they have a huge 600 gallon planted tank, i was like WHAO! when i saw that tank! lol
Also near in that same area Aquarium Village inc..473 Old Country Road, Westbury, NY, not impressed, small selection, but if you are in that area, could hurt to stop by and check them out.
Queens: Fishtown as mentioned by others...
Blue Gold Aquarium Inc.
8612 Whitney Avenue, NY
they have some harder to find fishes, ok prices
Kissena Aquarium Inc
4630 Kissena Boulevard, NY
Asian themed fish....blood parrots, flowerhorns, hybrids, ok selection, average price....usually negoitiable
Northern Aquarium Inc
13502 Northern Boulevard, NY
Another Asian themed fish place, ok selection, average price
As far as Manhattan, i have to agree with Hamsterguy....all 4 places i have been to, and are definitely places worth visiting. Depending on when you visit, you might find some nice interesting stock.
Well good luck on your adventures, and report back on any new finds...always willing to check out a good fish place.