I live in Staten Island and I have never been to a store in the city itself, but I do go to a few in NJ. Fishtown USA, Absolutely Fish, Reef Encounter, and The Pet Shanty. I have yet to try the Shark place on Rt 22- but I do want to get there.
I went to two stores in Long Island this past weekend- Aquarium Adventure and Petwarehouse.
On Staten Island itself Animal Kingdom is pretty good- although their selection can be sparse at times. You have to go there when they get fresh stock in or call ahead to see what they have.
There is a place called Arcadia Pets that is close to Animal Kingdom that is also good.
Lastly- the Petland Discount stores aren't bad and have a decent selection.