There is Petland Discounts at 510 5th Ave between 12th and 13th. They sell FW fish and some fish supplies. Buyer beware, though - their staff is woefully misinformed. I've seen them put dog harnesses on backwards...
No other stores that cary fish in the area - you have to venture further south. Look at this thread:
http://www.manhattanreefs.com/forum/...-brooklyn.html
And mandarin (below) is absolutely right - their fish usually look pretty sad.