The probe comes after an audiotape caught the boy directing several pilots preparing for take-off last month.
In one exchange, the boy is heard saying: "JetBlue 171 contact departure." The pilot responds: "Over to departure JetBlue 171, awesome job."
The boy was apparently with his father - a certified air traffic controller.
The adult is later heard saying with a laugh: "That's what you get, guys, when the kids are out of school."
In another exchange, the child says: "MS 4-0-3, contact departure," and then adds: "Adios, amigo."
The pilot responds: "Adios, amigo."
The pilots on the tape appear to be not concerned that a child is giving them instructions.
The incident happened on 17 February, when many New York pupils were on a week-long break.
The age and name of the child and the adult on the audiotape were not immediately known.
'Not indicative' incident
The Federal Aviation Administration said in a statement: "Pending the outcome of our investigation, the employees involved in this incident are not controlling air traffic.
"This behavior is not acceptable and does not demonstrate the kind of professionalism expected from all FAA employees."
The agency did not give any further details.
The National Air Traffic Controllers Association said the incident was "not indicative of the highest professional standards that controllers set for themselves and exceed each and every day in the advancement of aviation safely".