Within Manhattan...
New World has the best coral selection. It's not great. They are usually have a decent offering of LPS. Lately they have started to bring in more anemones, corals and clams, but still not much to speak of. They have a good and generally very healthy fish and invert selection. Their prices on livestock in general are high. Their prices on drygoods are insane. Their advice on livestock is genuine. Their advice on drygoods is also respectable, but they will not hesitate to trash a product that they don't sell, or when their margin is less. They are the only serious marine/reef store in Manhattan and despite the prices and occasional arrogance, a good place to spend your money, if you need to shop locally.
Some Petland Discounts shops offer a spotty selection of marine livestock. Sometimes healthy, sometimes not. Some stores have decent frozen food offerings, drygoods, etc. Drygoods prices are high, and selection is very FW oriented.
PetCo shops are really FW stores. They usually have several marine and brackish tanks, but stock is generally not healthy. You can always count on seeing dead marine fish.
Their are several small independant shops in Chin
atown. They are amusing and sometimes you'll find a gem.
Queens.
Aquatic Treasures has good coral and livestock selections. The owner is somewhat legendary in that he normally quizzes customers. He won't sell incompatible fish, and he won't even let you near the coral tanks until you've passed. He has a limited and usually expensive drygoods stock. This is not a fancy place like those you'll find on Long Island or in Connecticut, it's dimly lit, with a very DIY setup. This is a store/owner worth supporting if you can deal with the setup.
Brooklyn.
There are at least three stores in eastern Brooklyn with decent coral and marine fish selections. They are all within a mile or so of each other. The stores in western Brooklyn, closer to Manhattan are all FW oriented.