I think Scotts, in Westchester, is the best in the area. As others said...they have the best selection and very healthy fish and corals. They're located on 31st St., at the intersection of Wolf Road.
It's not that the staff is rude...they're just ALWAYS extremely busy, not like regular fish stores. I know 90% of the employees, personally, including Scott, the owner and they're all great guys.
I used to live in Riverside, which is only 20 min from Scotts. Now, I live downtown (over an hour away) and still make it a point to drive out there at least once a month.
Old Orchard Aquarium, in Skokie, rivals Scotts. For the hard to find, more exotic fish, go to Old Town. They're located on Skokie Blvd, one block north of Church St.