OK, first one from me: Fishtown USA
19633 Northern Blvd, Flushing, NY - (718) 539-5396
http://www.fishtown-usa.com/
This is the best store I know in city limits. It's not perfect, but:
- they have a lot of healthy freshwater fish, sometimes rare finds
-tanks are clean and fish that I bought from there were all in good shape
-livestock prices are in resonable level, plants, well, I've never found anything special or well priced
-that store is on a large side so it is a good place to just look around

-large saltwater section
Now cons:
-People working there are generally rude and don't care about you at all
-location of this store- if you don't have a car it will be PITA to get there, since there isn't any subway station nearby, only bus stops along the northern blvd
-equipment prices are generally high and they don't have good selection. What pisses me off is that they have a lot of equipment behind the desk so you have to ask the staff to take a look (and they wouldn't be happy to help you

)
Hope this helps