Two former NYPD officials and a Brooklyn businessman accused in a wide-ranging money-for-favors bribery scandal pleaded not guilty at their arraignment in federal court in Manhattan on Wednesday.

Now-retired Deputy Chief Michael Harrington and Deputy Insp. James Grant were charged last month with taking $100,000 in gifts from businessman Jeremy Reichberg and an associate, cooperating witness Jona Rechnitz. Reichberg and Rechnitz also have been linked to probes of Mayor Bill de Blasio’s fundraising.

The three defendants declined to comment while leaving court Wednesday, but Grant’s lawyer John Meringolo said the government had inappropriately turned police disciplinary matters — like ticket-fixing allegations and taking gratuities — into federal charges.

“It’s similar to what the FBI director said about Hillary Clinton and why she wasn’t charged,” said Meringolo.

The next appearance of Harrington, Grant and Reichberg was scheduled for Tuesday before U.S. District Judge Gregory Woods.