I live in a upscale apartment in NYC. I have opened my windows in the past few weeks due to the cool days and nights. One of my neighbors has a balcony in which he uses to smoke. The smoke smell fills my apartment every time the guy downstairs goes out to smoke. It is my understanding in my lease that no smoke smell may enter another room, or it is a violation of the lease agreement. Do I have any rights or am I to pay higher electric bills, suffer through the smell and subject myself and my family to second hand smoke?

The other people are going outside to smoke. You choose to open your windows. You can't prohibit them from smoking outside the building, only inside the building.

Sorry if the smoke does not enter your apartment with the windows shut, it is not a violation

Yes, you do have rights. The harm must involve more than a slight inconvenience or petty annoyance. Unless you can prove that your neighbor's act is deliberately causing smoke to contact you, your neighbor is within his/her rights. Possibly venting air through another window may help. The provided link may help in finding a peaceful solution to help resolve this issue.

Neighbors File Lawsuit Over Smoker's Stench - Total Injury