I'm pretty sure you can only smoke cigarettes in Marshall McGearty's. I was there, and one of the staff intervened when some guys tried to light pipes. I'm pretty sure I heard her say that the place was cigarette only.
There's a tobacconist on Damen a few blocks south of Le Bouchon, but I don't care for it, and they've been rude to me. Casa Del Tobacco on North (right next to Santulo's) is a very nice shop with a courteous staff and a good selection.
Not sure which bars around there are cigar-friendly with a decent scotch selection. The California Clipper at Augusta and California has a decent selection, and they have no problem with stogies.