Best Butcher Shops
I've been using Holland Court more and more on Lexington and 93rd St. Doesn't look like much from outside, but the meat is v. good and they can get anything for you. I also like Ottomanelli on Bleecker, and Florence Meat Market on Jones Street. Schatzies - he's moving to the UWS from Madison Avenue - is another butcher I use.
Lastly, I would say that Lobel is probably the best in Manhattan, but at quite a price.
For the other boroughs, you'll want to post on the Outer Boroughs board.