There are a few nice shops in Manhattan. Nat Shermans on 42 St and 5th Ave is nice. If you go on Thursday nights, they always have a herf with some sort of wine or scotch, you get 2 smokes and drinks for $25. I like Nat Sherman cigars so it's nice, but they sell other brands. You also have Barclay Rex. I go to the one on Broad St (75 Broad I believe). Slightly pricey, but top notch smokes and very good quality.
If you want to hang out and smoke for a while, try the Wall Street Humidor at 18 Warren St. (near cityhall). No alcohol served, but they don't mind if you bring something in with you. If you have money, there are a few Davidoff Shops and De La Concha (6 Av and W 58 St). Just to name a few.....