Authorities suspended the controller and a supervisor Wednesday after a recording of the radio calls was posted on the Internet, then reported by a Boston television station.
"This lapse in judgment not only violated FAA's own policies, but common-sense standards for professional conduct. These kinds of distractions are totally unacceptable," FAA Administrator Randy Babbitt said in a statement. "This kind of behavior does not reflect the true caliber of our work force."
During his visit, the boy got to squeak out a few more instructions to pilots before signing off, including telling the crew aboard a departing Aero Mexico flight, "Adios, amigos."
On the recording, which lasts about a minute, the elementary-school-age boy appears to repeat instructions fed to him by his father. At no time does the child tell aircraft how to maneuver in flight.
At the time, pilots appeared delighted.
"I wish I could bring my kid to work," one said.
Nevertheless, the FAA said it has also barred unofficial visits by friends or relatives to FAA air traffic operational areas while it reviews its policies.
Radio transmissions between air traffic controllers and pilots are routinely streamed live on the Internet. A user of one popular Web site devoted to controller talk, LiveATC.net, posted a recording of the child's radio calls not long after they happened on Feb. 16 - a date when many New York schoolchildren were on a midwinter break.
The boy made five transmissions to pilots preparing for departure, according to the recording.
"JetBlue 171, cleared for takeoff," the boy says in his first call. His father follows that up with a more detailed instruction for the aircraft, which was headed to Sacramento, Calif.
He then offers an explanation to pilots on the air: "This is what you get, guys, when the kids are out of school."
In a second exchange, the boy instructs the same JetBlue flight to contact departure controllers. The pilot responds: "Over to departure, JetBlue 171. Awesome job!"
There are a few more similar exchanges. A pilot laughs. The boy can be overheard giggling.
Based on the flight numbers called out during the exchange, the episode appears to have happened in the early evening, when JFK is often bustling with international flights.
The FAA offered scant detail on its investigation and would not reveal the name of the controller or supervisor. Control towers are highly secure areas, although the agency does sometimes give employees permission to bring their children for a tour.
The union representing air traffic controllers condemned the worker's behavior.
"It is not indicative of the highest professional standards that controllers set for themselves and exceed each and everyday in the advancement of aviation safety," the National Air Traffic Controllers Association said in a statement.
LiveATC founder Dave Pascoe, a pilot and radio enthusiast, said he was sickened at the thought that the controller could be disciplined.
"I absolutely believe that this is being blown out of proportion," he said. "This is just a completely controlled situation. A child was being told exactly what to say."
He added: "I think it's just fantastic that this guy cared enough to take his kid to work. How many parents take their kids to work these days?"
The episode comes less than seven months after a controller at an airport in nearby Teterboro, N.J., was placed on leave for his actions in the moments leading up to a deadly crash between a helicopter and small plane over the Hudson River.
The controller was recorded joking on the phone with his girlfriend as he dispatched instructions to the doomed plane. He ended the call when he realized the plane had dropped out of radio contact, just seconds before the crash.