Kelly spoke with CBS News' Scott Pelley in an interview for 60 Minutes about the NYPD's counterterrorism unit, which was created after September 11.
Here's the key part of the transcript, via CBS News:
Pelley: Are you satisfied that you've dealt with threats from aircraft, even light planes, model planes, that kind of thing?
Kelly: Well, it's something that's on our radar screen. I mean in an extreme situation, you would have some means to take down a plane.
Pelley: Do you mean to say that the NYPD has the means to take down an aircraft?
Kelly: Yes, I prefer not to get into the details but obviously this would be in a very extreme situation.
Pelley: You have the equipment and the training.
These comments come in around the 5:16 mark: