The breach of security regulations delayed the flight by nearly an hour and prompted a Transportation Security Administration investigation of an airline employee.
The American Airlines worker escorted the reality-TV star and the singer through a nonpublic area and onto a flight to Los Angeles in violation of TSA protocols, the source said.
The agency said in a statement that the passengers, whom it did not name, arrived at Kennedy on a flight from Rio de Janeiro and cleared U.S. Customs and baggage recheck. Then the airline employee took them through a nonpublic area to provide "expedited access" to their domestic flight.
In doing so, West and Kardashian were allowed to board the flight without going through a TSA security checkpoint, the TSA said.
When agency officials learned of the violation, officers removed the couple from the flight and screened them in the jetway, the TSA said.
The flight was delayed for about 50 minutes.
"This was a lapse in judgment by one of our employees," Matt Miller, a spokesman for American Airlines, said in an email. "We're working closely with the TSA and speaking to the individuals involved to better understand what happened."
Representatives for Kardashian and West did not respond to requests for comment.