Nat Sherman is the best in terms of atmosphere and browsing. It's stepping back in time. The other options (Barclay and Davidoff) are more of a luxury accessories shop now with tobacco. But Nat Sherman is proper tobacconist and has the best selection of bulk blends. You'll be a fan of #536 if you like Balkans. The seating isn't necessarily a lounge though. It's a few chairs in the middle of the store. There's also a proper smoking lounge/bar in the basement but it's not always available to use. If you have questions about anything, ask for Michael Herklots. He's sort of a big deal in tobacco retail now and has a HUGE knowledge of tobacco.
Davidoff on 6th Ave has a nice seating area and a small but solid tinned tobacco selection. It's pricey, but they had some Christmas Cheer and other limited tins. Ask for Kevin if you have questions about pipe tobacco there.
Davidoff at the WTC is pretty much a bust unless you're in the WTC area. Limited tobacco selection (maybe 4 tins total on display?) The lounge is pretty nice though. And there's lots of food options around. Le District, in the same mall, has lots of craft beers and food. But again, only go there if you're looking to buy a majorly overpriced pipe or one of four tins of tobacco.
Barclay Rex in Financial District (their only location now) is a great option. They have a strong tin selection and several house blends. You can find most of their blends on tobaccoreviews.com. I'm a fan of Maiden Lane. It's a Frog Morton type smoke. There's also a lounge in the basement.
My two cents:
If you're looking for an old fashioned tobacconist atmosphere with a good selection for browsing, Nat Sherman.
If you're looking for a solid choice of tinned tobacco and an "ok" place to smoke downtown, Barclay Rex.
My personal suggestion would be to purchase some tobacco at the Nat Sherman townhouse and then walk up to the Carnegie Club. It's a huge, 1920's looking cigar lounge. They have killer cocktails, a satisfying food menu, and plenty of comfortable seats. If you're there on the weekend they also have live jazz and/or Sinatra tribute shows.
And just so you know, all of this will be pricey.