While you would not be able to enter the secure area, your niece can join you outside of it in the concourse of any of the JFK terminals. Indeed, her flight from Florida may arrive in a different terminal from that of her onward flight to Israel, and she would need to make her way from the arrival terminal to the departure terminal. In that case, she would have to go through security at the departure terminal.
Most trans-Atlantic airlines from JFK recommend arriving at the airport a minimum of 2 hours before flight departure and going through the check-in/security processes. At that time of the morning, 2 am, she should be able to go through security fairly expeditiously but, to be safe, she could use the TSA online tool to view security wait times at her departure terminal.