It's no more hypocritical than a community banning the sale of liquor at restaurants, but letting people bring their own liquor to drink.
So, apart from the hypocricy in allowing the sale but not the smoking of cigarettes in public accomodations, you have no problem with a city prohibiting the smoking of cigarettes within its limits?
You got your hypocrisy backwards. According to your example, Mr. Bloomberg would ban the sales of cigarettes yet allow people to smoke them. I'm saying the hypocrisy is in profiting (actually profiteering) from the sales of cigarettes, then not allowing people the opportunity to smoke them.
Now, from a city that banned a constitutional right to keep and bear arms, banning cigarettes would be a walk in the park. But if New York City continues to sell cigarettes, I would find the message to be disingenuous at best. If I were a voting resident of New York City, I would not vote for prohibition.