I have had very good luck recently with a few fish stores:
Pets of NH Park.. I bought an Acan frag for a good price. It's doing well. Their staff is friendly for the most part. Don't agree with the puppies. (People shouldn't buy the puppies directly either)
Pets Warehouse has friendly staff. Decent selection. (I especially like their frag racks). Prices are decent. Most fish are healthy looking. I've had good luck so far.
On to my two favorite stores in the area:
Tropical Island Aquarium on Rte 231. Excellent store. Good selection (even though it's a small space).. Good prices. Healthy Fish. The help is very friendly.
My favorite store around though, hands down, is Manhattan Aquariums. (Also Unique Corals. (.com). Their selection is incredible. They have jaw dropping colors, rare pieces, and a range of inexpensive (for NYC) to super expensive. There's a number of Huge, amazing looking display tanks. Very healthy fish, (great selection too) and very friendly staff. I'd recommend anyone who's making a stop in NYC to head over and pay them a visit.