I just got back from a trip to Vestal and Binghampton.
I wouldn't call any of the shops nice, but they are good for the area. I haven't been to the stores in Syracuse or Buffalo so I don't have much to compare them too. I'm from Ithaca and the one store we have is pathetic. The fish are usually on sale, but are so sketchy I won't take the chance.
Natures Best Fish is one of the better stores I've been to in the area. They know about fish, gave me some good advice, and are nice. They have a research area where they test new equipment and are working on some food, so that was interesting. Also, they give you 20% back on livestock for future livestock purchases. Lots of fish and live rock, a few corals, nothing too special.
Creature Comforts is a mini chain store. They have tons of supplies, small fish selection but the fish are alright, coral not so much. They did have some interesting stock I hadn't seen elsewhere, but not worth a special trip. I ate at the spiedie place next door, it's pretty good.
Livingstons Animal Kingdom, had a few nice fish. Not too knowledgeable though. Sold me a Blue Stripe Nudibranch and told me it ate algae. It eats white sponges and fortunately I have lots.
I wish there were more. I usually travel from Ithaca to Tropical Fish Outlet in Elmira or Tropical Fish Emporium in Auburn. They aren't the greatest stores, but the owners and employees are really nice and knowledgeable. TFO in Elmira is probably my favorite. Lots of fish and nice coral. It's a little expensive though.
Enjoy! If you find a good store that I missed, please let us know!
James