When I last went to NY (about 18 months ago), I did some extensive research into exactly the same question. And suprisingly there are some good BBQ restaurants in Manhattan, and not only that my favourite was just off times square (I know, I thought here we go, complete tourist trap). However, I visited this restaurant 2x and both times it was excellent. The chicken wings were excellent as a starter and the meat platter (I think its the pig out and it was under $30) was a taster of everything and could easily feed 2 was a really good way to experience all meats. Still seems to get solid reviews on the web. Give it a go is my recommendation. Its Called Virgils
http://www.virgilsbbq.com/The other restaurant I went to was Brother Jimmy's. The deep fried onions were out of this world but the BBQ was average at best.
http://www.brotherjimmys.com. Saying that it was still better than Bodeans
Blue smoke has good reviews, I have never visited it the restaurant, but chums have and said food was good, but a little pricy (ie upmarket bbq?).
http://www.bluesmoke.com Have a great trip!