“They would be worth considering under many circumstances,” Mr. McQuaid writes. “In today’s dark times, they are a bright light of hope and reason.”

The Union Leader endorsement could make an impact in the hard-fought contest in New Hampshire: An NBC News/Wall Street Journal/Marist poll of likely voters from earlier this month showed Hillary Clinton with a slim, two-point edge on Mr. Trump, with Mr. Johnson capturing 15 percent of the vote. Enjoying the support of The Union Leader, with its recurring front-page editorials reaffirming its choice, could give Mr. Johnson a lift in the Libertarian-leaning state, draining votes from Mr. Trump (and potentially from Mrs. Clinton).

Newspaper endorsements have considerably less currency now than in an earlier political era, of course. The Union Leader’s backing of Gov. Chris Christie of New Jersey in the state’s primary did little for his campaign and their regular broadsides against Mr. Trump did not stop him from rolling to a 19-point victory there.

But in withholding the paper’s endorsement of Mr. Trump, Mr. McQuaid, who has sparred more than once with the Republican nominee on Twitter, is attempting to get in a final word with his New York nemesis.

“Voters leaning toward Trump are understandably fed up with the status quo, of which Clinton is a prime example,” he writes. “But they kid themselves if they think Trump isn’t pretty much a part of that status quo as well, or that he is in any way qualified to competently lead this nation.”