You'll take a hit selling to a shop for sure. At some, you'll do better taking it in trade if they have something you want. But the amount they're giving you will go soft if you demand that they match internet prices for the item you trade for. To be fair to them, they're a business, not a charity. Depending on New York law (I wouldn't know, not living there) they may have to hold it for some period (30 days?) to make sure it hasn't been reported stolen, for starters, during which time it will be taking up floor space and tying up capital.. After that, they are assuming the risk that it may not sell quickly. They have to pay overhead costs that online sellers may not (rent, insurance, employees, etc.). If they are Fender and/or Gibson dealerships, they are forced to take an arbitrary, non-trivial number of new instruments, dictated by those companies, into inventory every so often. Keeping a brick-and-mortar music store in business in the internet age has got to be a tough assignment.
I'd go CL if your item is something that's a huge hassle to ship, or Reverb or here if not.