I assume you're a US citizen and that your bags can be checked through to their final destination. I see no reason why you can't leave the airport if the above is true.
Figure about 90 minutes to get from JFK to Times Square. It could be less if traffic is light based on the time of day. Figure another 90 minutes to return to JFK. Also remember that for International Flights you have to be at the airport a couple of hours before your flight, to go through security screening and the like.
So, if your plane arrives on time and your next flight is expected to depart on time, there is more than enough time to visit Times Square, or somewhere else in Manhattan, if you have the energy.
You may want to figure out exactly what you want to see. Times Square is just a district in Manhattan. Lots of stores, but there are similar stores elsewhere.
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