IST has fast track transfer security checks (for Business class and Elite/Star Alliance Gold) and short connection time transfer checks (look for it when you have entered the terminal and walking towards transfer security) BUT if you arrive from a "clean" country (e.g. from Europe) you will be lead straight to departures level and do not have to pass security checks. MCT at IST is 1 hour so your connection is valid and most likely you will make it; I wouldn't worry too much about.

If your incoming flight is late and you miss the flight to JFK TK will rebook you to the next JFK flight; there are several flights a day so not the end of the world.