There's also a place in the West Village called Bone Lick that is hit or miss - but really quite good on the days it hits. And don't forget Dinosaur BBQ way uptown by Fairway. Off most people's path for sure, but good 'cue.
Virgil's is good as well, and was my standby before the current crop started opening maybe four years ago. I can't say that, with the other options, I would still choose to go near Times Square for BBQ ;-)
For another poster that asked about Dallas BBQ and Spanky's - Dallas is for when you can't afford real BBQ. It can be reasonably good and I enjoy the Honey BBQ basted chicken, but with an avg. check of under $10 in Manhattan, you canb't be expecting very high quality ;-) And Spanky's, owned by Heartland Brewery, doesn't cut it IMHO. I like Heartland and their beer, but tried the 'cue twice and will pass on more.