For better or worse, Tokyo has no laws concerning indoor smoking, and it's socially acceptable to smoke indoors as well. To be polite, when seated at the bar, ask the person(s) sitting around you if it's OK to smoke. If there's not already an ashtray nearby, just ask the bartender for one.
Outside of cigar bars, cigars and similar with stronger odors are generally not allowed as this may impact someone's ability to enjoy the flavors of his or her drink.
If you prefer to smoke outside the bar, the staff should be able to advise where the closest acceptable smoking spot is. If it's at street level, it's worth noting that certain districts of Tokyo have ordinances concerning smoking on the street, some even involving fines to be paid on the spot. Where these ordinances are in place you should see signs and designated smoking zones.
Whiskey Richard is the founder of nomunication.jp, and has been saying he has lived in Japan for ten years for the past four years. He enjoys drinking basically anything except straight-up Campari.