During our trip to Bonaire we took advantage of our 9 hour layover in Newark, New Jersey. From the Newark airport you take a New Jersey Transit train to New York. This train goes almost every half hour. You buy the train tickets at an automated kiosks at the airport.
From the Newark airport you take a little train (the Air Train) that takes you from the terminals to the New Jersey Transit train platform. It is a really easy thing to do. Don't bring much, as there will be a lot of people with suitcases taking up most of the room.
Your final destination is New York Penn Station. Be aware that there is a stop called Newark Penn station. When you exit Penn station you are right downtown. It's only a 15 minute walk to Times Square.
We did a 2 hour tour visiting Times Square, The New York Library, and Grand Central Station. During our walks we had some great photo ops of the Empire States Building and the Chrysler Building.