Usually 3 hours before the first evening flight. If in Upper then they generally take your bags any anytime otherwise they are reluctant to take them before 3 hours before your actual flight.

I'm sure there is something on the JFK page on the VS website about check-in times.

What time is your flight? If you are arranging at JFK at 11am you might want to look at putting them in the left baggage and then going into Brooklyn / Manhattan rather than hang around JFK