If you don't have much luggage, I'd just take the 7 Express train from Times Square. You'll ride it to Mets-Willets Point, then transfer to the Q48 bus.
The Google says the 7 Express will take 26 minutes, and the Q48 will take 11 minutes. With some walking and transfer time included, you can rest assured you'll make it to the airport in 50-60 minutes with no risk of traffic.