For LFS (local fish stores), I prefer to go to chinatown as they don't charge tax and you can haggle them to lower prices sometimes. Heres a list of them and their addresses to help: In or around Chinatown
Win Tropical Aquariums
169 Mott St
(212-343-2875) Pretty nice old couple that runs the store and are pretty helpful. You even get to pick out the fish yourself so you know you're getting good ones.
Aqua Star Pet Shop
172 Mulberry St
(212) 431-4311 Around the block on the other side of Wins, very small store. The owner looks sort of like Mr. Miyagi from "Karate Kid". Good fancy goldfish variety with the usual fish.
38 Aquarium Inc
371 Broome St, New York, NY
(212) 966-0397 On the corner near Wins, sometimes an old guy is there and the other times, this guy with slicked hair who chain smokes all day. I prefer not to go in there but they have very good discus for cheap prices, sometimes $20 when they're on sale. The chain smoker seems grumpy and doesn't seem to like kids or teenagers. Other than that, the store has predominantly flowerhorn fish but also has koi, 2 huge display tanks at the windows filled with probably over 400+ small fancy goldfish. Very good discus again, probably the only reason why I go into that store.
88 Aquarium Inc
123 Elizabeth St, New York, NY
(212) 431-0777 Small store, not much variety. Just flowerhorns, red parrots, some discus and plecos.
Pacific Aquarium & Pet Inc
46 Delancey St, New York, NY
(212) 995-5895 Has fresh and salt water fish. Very helpful staff and an amazing planted tank that has rare plants. Good variety of fish and supplies and cheapest for flourite (I haggled them to $16 a bag), that and I'm not too sure other places carry it. They also have eco-complete and most fish are buy 2 get 1 free. The only asian place that carries a decent variety of plants. Midtown
New World Aquarium Inc
204 E 38th St, New York, NY
(646) 865-9604 Extremely high priced. Good variety of fresh water stuff but excellent for salt water tanks. For some reason, I get this feeling everytime I walk in that I'm not well liked in the store or something. I'm a college student with a low budget and I just like look around the store, but they always seem to ask if I need help in a way as if they're expecting you to buy something. Again, extremely expensive but very good variety of fish and a pretty decent variety of plants, they can order if you need. Uptown
(On the East side of Broadway, 98th-99th)
212-865-7500 Haven't been. Brooklyn
99 N 10th St, Brooklyn, NY
302-9080 Salt and fresh water tanks. Nothing good or bad to say about this place, just went there to help a friend carry a tank home. Fresh water doesn't have much variety, its mainly a salt water place. Queens
Fish Town USA
19633 Northern Blvd, Flushing, NY
539-5396 Haven't been either, but I hope to some day.
Also, theres various Petcos and Petlands around Manhattan. Petco on 86th and Lexington, 33rd and 2nd ave, and another one near I think 82nd and Broadway. Petlands on too many to name, just find one and look for the rest on the bag. Hope you have fun traveling the city and looking at fish stores. I've been to more but just don't really remember them, yea...pretty sad that I like to spend time finding good fish stores. There's a lot of other fish stores besides the few that I've listed but these should be enough for just about anything. Anyway...hope this helps.