I've been to many of the shops here in the NYC area. Here's my take on some of the stores I've visited this year:
Absolutely Fish - I was in North Jersey and made a special trip there after reading so many good things about it. I didn't leave there very impressed. In fact, it was a wasted trip.....but at least I know I won't have to go back there again. The store was clean and the livestock looked okay. Not the selection I expected and prices weren't very good at all.
Aquarium Adventure - I live in Queens and have been there quite a bit over the last few months. This is the only store I've found that stocks SAEs. I got mine there. This is easily the cleanest LFS I've been to. The selection of fish is amazing and all of the fish are healthy and active. The store is huge and layout is really nice. Livestock prices are decent, not the best but they aren't too bad. This is probably the best store I have visited thus far.
Fishtown U.S.A. - I work about a 15 minute drive from there. I have never bought anything from there and doubt that I ever will. It seems as if just about every freshwater tank is cloudy and there are dead fish all over the place. The fish do not look very lively either. They did have some realy nice Gold Nugget Plecos in there last weekend. I think the best bet to to buy fish when they first get there and the QT them yourself at home. A nice place to check out if you're bored, but that's about it.
Petco - I'll mention the good and bad stores I've visited:
Good: Valley Stream, Westbury, Howard Beach, 5 Towns, Deer Park
Bad: Levittown, Garden City Park
Petland Discounts - For the most part, all of these stores are horrible. I have found a few exceptions. The store in Valley Stream (next to Walmart) has a decent selection of fish and pretty healthy looking tanks. The other store I like is in Great Neck. Not the greatest selection of fish, but the tanks are clean and the fish I have bought there are healthy and still doing very well.
Pets of New Hyde Park - This is probably the #2 store behind Aquarium Adventure, but it is my favorite store to visit. I have probably bought more of my fish from here than anywhere else. They have a really good selection of fish and THE best selection of African Cichlids I've seen in ANY store. This is also the only shop I've been able to find Kuhli Loaches in. Tanks are well maintained, fish are lively and healthy, display tanks are pretty cool, and the pricing on their livestock is very good.....but don't even think about getting food or equipment there unless your last name is Trump!
Petsmart - I've been to stores in Levittown, Huntington, Paramus, and New Brunswick.....they are all about the same. Great for pricematching, okay for food selection, decent pricing. Buy livestock at your own risk.
Tropical Showcase - Similar to Fishtown but without the crappy tanks and dead fish. Tanks looked better but nothing that makes me want to go back there. I'll drop in if I'm in the area from time to time. I have yet to be impressed.
Walmart - Yes, I have bought fish here too. The Valley Stream store used to be really good. At one time, they had some pretty knowledgable people working the fish section and there was always someone there cleaning or changing water on the tanks. They have since moved the tanks during a rearrangement and I haven't seen the people who worked that section there anymore. As a result, the tanks have looked like crap lately. I have gotten some nice Otos and Cherry Barbs from there, but I will not be buying from them anymore. This was the only Wally World store in the area worth buying nything from.