No, the ban appears to be total. (Even if there are a few bars defying, or somehow avoiding, the ban, they are probably so crowded and toxic, that you probably wouldn't want to stay in them for very long.)
I was in Manhattan about 2 weeks ago and again a month before. Both times i heard about a cigar bar in the Davidoff store, they said its very nice and not too crowded OR toxic (obv depending on times of the day etc) although i didnt get a chance to get there myself.
I also noticed that many restaurants still allow smoking if the tables are outside and either well spaced or away from others... good luck and let us know the outcome :)