PATERSON, NJ – Mayor Jeffrey Jones’ decision on Thursday to endorse Steve Rothman instead of Paterson’s native son, Bill Pascrell, stunned his closest political allies and may have caused hard feelings that could linger long after Tuesday’s Democratic congressional primary.

“He’s taking the risk of losing a lot of allies,’’ said Assemblyman Benjie Wimberly, one of the strongest supporters of the Jones administration these past two years. “He’s taking a major gamble on a roulette wheel and putting a lot of money on a number. The odds are against him.’’

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“The election has more to do with the prosperity of Paterson than it has to do with Pascrell the individual,’’ said Freeholder Theodore Best, who had supported Jones’ 2010 election campaign and also once worked on Pascrell’s staff. “Even if the mayor has problems with Pascrell the individual, he can’t deny that Pascrell the congressman has worked to benefit the City of Paterson.’’

But Jones does deny that. In an interview on Friday morning, Jones insisted that his decision had nothing to do with personal conflicts and everything to do with what he thinks is best for Paterson. Most of what Pascrell has done for Paterson “is just doing his job,’’ the mayor said.

“It’s the stuff that goes above and beyond that matters,’’ Jones said. “In most states, the top three urban centers usually do very well (getting federal funding). But we haven’t seen those benefits. Nobody should have to endure what we endure.’’

Jones also said he was frustrated by city political leaders’ reaction to his endorsement. “It’s almost like a bully pulpit, they’re trying to force people into doing and saying the same thing,’’ Jones said. “Where did all this lockstep stuff come from?’’

“This is a primary, right? I’m supposed to be able to support whomever I choose,’’ Jones said, asserting that Pascrell himself made that same point during a candidates forum sponsored by the Paterson Pastors’ workshop in explaining his 2008 endorsement of Hillary Clinton over Barack Obama.

During the past five months, many city political and community leaders have described Pascrell’s success in the primary as essential to Paterson’s well-being. They have warned that the city would become a political stepchild if Rothman from Bergen County were to win. All of Jones’ closest political allies have campaigned for Pascrell. In fact, the only city officials besides Jones who have backed Rothman were members of the Dominican caucus, a group often at odds with the mayor.

“I’m having a difficult time wrapping my head around this one,’’ said the city’s Democratic Party chairman, Errol Kerr. “It makes sense for the Dominicans because their base is not supporting Pascrell. But Jeff’s base is supporting Pascrell. There’s a contradiction here.’’

“How is this going to affect Jeff later on down the road? I don’t know,’’ added Kerr, who also serves on the city school board. “A lot of people are going to remember that and take it seriously.’’

Passaic County Democratic Party chairman John Currie would only discuss Bill Clinton’s endorsement of Pascrell, including his scheduled campaign stop at Kennedy High School on Friday, rather than the local political ramifications of Jones’ decision. “This is so much larger than Jeff Jones,’’ Currie said.

Wimberly said Jones was alienating his own supporters by backing Rothman. Some people who backed Jones in 2010, when he won by less than 500 votes, already have jumped ship. The mayor has taken criticism during his first two years in office for various issues, including a cumulative 33-percent tax increase and the controversial overtime checks issued to himself and his Cabinet.

“The people are going to take what they want from the mayor’s decision, but he has the right to support whomever he wants,’’ said Erik Lowe, Jones’ good friend and chairman of the Paterson Municipal Utilities Authority. “After June 5, there’s going to have to be a healing process, with the mayor and the Democratic elected officials and the Pascrell supporters.’’

“I believe it’s going to be a strenuous situation because 99.9 percent of the people in Paterson are behind Bill Pascrell,’’ said veteran city Councilwoman Vera Ames-Garnes. “But his belief is his belief. You’ve got to be true to yourself.’’

Assemblywoman Shavonda Sumter, who had been Jones’ mayoral campaign manager, was one of many people who said she was caught off guard by Jones’ announcement of his support for Rothman. “I thought he was going to remain neutral,’’ Sumter said.

When asked whether the endorsement would hurt Jones, she replied, “There’s always consequences for every action taken. But he’s entitled to his choice.’’

 Sumter and Wimberly said Jones had not discussed his decision to back Rothman with them. “He should have been more of a leader and sat down and discussed this,’’ said Wimberly. “Maybe he would have brought up some points that would have changed people’s minds.’’

But Jones said he had not considered conferring with other city political leaders before making his endorsement. “Why should I? They didn’t ask me before they endorsed him (Pascrell),’’ said the mayor.

Jones asserted that Wimberly and Sumter were both newly elected officials who had not been directly involved in government as long as he has. Jones said he was in better position to judge Pascrell’s performance for Paterson. “They can’t tell me about what I know. I’ve been there.’’