Other U.S. airports identify with places where they aren’t located. San Francisco International Airport is in another county. The Providence, R.I., airport is in Warwick, R.I. Cincinnati’s airport isn’t even in Ohio. It’s in Kentucky.

Newark is being dropped from the group of airlines that share the New York City code for technical reasons by the International Air Transport Association. The change, slated for April, should be largely invisible to consumers. Travelers will still see Newark as an option when they search for flights to New York.

The Justice Department doesn’t consider the Newark hub one of the New York City airports for domestic travelers, according to an unrelated antitrust trial under way in Boston. The government has a case against a planned partnership in the northeast between American Airlines Group Inc. and JetBlue Airways Corp.

Both airlines operate out at LaGuardia and John F. Kennedy International airports in the New York City borough of Queens. The government claims that by joining forces, the two companies will limit competition in New York.

The Justice Department said the New Jersey airport serves a different customer and should be considered a “distinct endpoint” for U.S. fliers.

The two airlines argue the omission paints a skewed and inaccurate picture of the New York air-travel market.

On Wednesday, the debate triggered a minor courtroom drama. A Justice Department lawyer quizzed JetBlue CEO Robin Hayes about a 2020 presentation that touted the airline’s position as New York’s second largest carrier by domestic capacity. The claim didn’t include the Newark airport, which would have dropped JetBlue lower on the list.

“With hindsight, we should have included Newark,” Mr. Hayes said.

The Justice Department declined to comment.

Mr. Hayes testified that JetBlue customers see Newark as a New York airport. “Everyone in New York I believe understands that,” he said.

That may be, but a lot of airline passengers aren’t happy going through Newark. A J.D. Power Survey this year ranked the airport lowest in customer satisfaction among major North American hubs. The survey was done before the completion of renovations there.

“You can get in and out of Newark airport better than you can get in and out of any New York airport,” said Mr. James, the former mayor. “If anyone wants to debate me on that, I’ll take all comers.”