One-time acting Genovese boss Liborio “Barney” Bellomo has to be kicking himself for taking what seemed like a sweet plea deal: about four years in prison for a host of racketeering charges, including a 1998 murder for which he once faced the death penalty.

The deal looked a lot less attractive last Thursday, when the cagy gangster learned that the government’s murder case had fallen apart and that prosecutors were concerned that he could win an outright acquittal. Barney got the news directly from the horse’s mouth.

At a remarkable court session, an assistant U.S. attorney, Miriam Rocah, disclosed that authorities were also fearful that their key witness against Barney, an aging and ailing turncoat mob lawyer, Peter Peluso, might not be able to survive a trial appearance.

Even if Mr. Peluso, who suffers “a serious kidney condition,” was able to get through tension-filled court sessions every other day — he undergoes dialysis treatment “three times a week, several hours a day, and it essentially wipes him out for that day,” Ms. Rocah said — the case was still in dire straits, the veteran prosecutor declared.

She disclosed that the federal investigators were never able to locate prison records they “were hoping to get” to back up the murder charge, which was based on “essentially one conversation between Peluso and Bellomo” that allegedly took place while Barney was housed in a New Jersey state prison in 1998.

“It was, frankly, kind of a bitter pill for us to swallow,” Ms. Rocah said. “It basically was a weighing of particular litigation risks that became more clear to us as we prepared and got closer to trial against the certainty of this conviction, albeit not the conviction we would have wanted, but a conviction,” she added.

Ms. Rocah and her co-prosecutors were forced to publicly disclose the failings of their case in U.S. District Court in Manhattan by Judge Lewis Kaplan, a usually pro-government jurist. He called them on the carpet to explain why he should accept a guilty plea that would mean about “three-and-ahalf to four years” behind bars for a mobster originally charged with murder.

Judge Kaplan has a reputation as a dogmatic jurist who has been criticized by the Second Circuit Court of Appeals for overstepping his bounds. Last month, the appeals panel warned him for instructing 16 defendants in a $2 billion tax fraud case to file a civil suit against their employer, and then declaring that he would preside over the new case using a mix of criminal and civil rules of evidence.

Judge Kaplan, who had accepted a 10-year plea deal from Barney in 1997 to resolve a 1991 murder charge that the gangster vehemently denied, couldn’t wait to voice his intention of rejecting the current plea bargain.

A day earlier, during a conference with lawyers for the Genovese family’s current acting boss, Daniel “The Lion” Leo — with neither Bellomo nor his attorneys in attendance — Judge Kaplan told Ms. Rocah’s co-prosecutor, Eric Snyder, that he was inclined to reject Bellomo’s plea deal, and instructed Mr. Snyder to plan to bring Bellomo, 50, and Leo, 66, to trial together in November.

When Mr. Snyder informed the judge that the charges against both mobsters were unrelated and that he hadn’t even considered consolidating their cases, Judge Kaplan declared sternly: “Think about it.”

Just to make sure Mr. Snyder understood exactly how long and hard he should think about it, Judge Kaplan brought the subject up again after concluding preliminary discussions about Leo’s bail status.

“I am going to see you tomorrow,” the judge said. “I am very interested in why I should take a plea to a mail fraud. This is the second time the government has done that with Bellomo before me. I am mighty curious as to why I should accept it.”

The following day, Ms. Rocah, who stressed the government’s inability to prove the murder charge rather than Barney’s innocence, recited the government’s view. Bellomo’s lawyers, Richard Levitt and Barry Levin, gave numerous reasons why they believed he was indeed innocent of the slaying of capo Ralph Coppola.

Mr. Levitt noted that in Mr. Peluso’s first interview with the FBI, when he was selling himself as a potential witness, he told agents that Barney had nothing to do with the murder. Not only were there no records of any visits to Bellomo by Mr. Peluso, Mr. Levin added, three prison guards would testify that the visiting area bore no resemblance to the layout that Mr. Peluso described.

As it happens, the feds got their deal after all. In a one-page ruling Tuesday — without making any mention any of his prior reservations — Judge Kaplan decided that the prosecutors had good reason to offer Barney the plea bargain.

Bellomo is currently serving a four-year stretch as a result of a separate plea bargain, this one struck in U.S. District Court in Brooklyn. That term ends in 13 months. He will be sentenced on the mail fraud case on July 9.

A RECOMMEND BY ANY OTHER NAME . . .

As Gang Land disclosed two weeks ago, Barney’s plea deal states that he and the feds agree that his sentencing guidelines call for between 41 and 51 months behind bars, and that neither his nor the government’s lawyers will recommend any specific prison term.

In her efforts to mollify Judge Kaplan’s concerns that Bellomo wasn’t getting his just desserts, Ms. Rocah may have violated the spirit, if not the letter, of that agreement.

When the prison terms of the three plea deals were added together, she noted, Barney would serve 17 consecutive years if the judge were to ignore the sentencing guidelines and mete out a five-year (60-month) sentence.

“I mean,” Ms. Rocah explained, “he’s facing up to five years here, so I’m using that outside limit, because it’s a five-year statutory max. He could serve up to 17 years.”

FBI CASE JUDGE MAY WHACK A SECOND MURDER CHARGE

For the Brooklyn district attorney’s office, it’s déjà vu all over again as another murder indictment related to the pending prosecution of a retired FBI agent, R. Lindley DeVecchio, is in danger of being thrown out.

Still reeling from last week’s stunning dismissal of a murder charge tied to the ex-agent’s case, Brooklyn prosecutors are locked in a court battle to convince a judge to accept the validity of a second murder indictment and not toss it for the same reasons the charges against John “Johnny Loads” Sinagra were dropped.

In 2006, Craig Sobel was accused of the October 31, 1989, slaying of Dominic Masseria, but an attorney for Sobel, Toni Marie Angeli, contends that prosecutors violated her client’s right to a speedy trial by failing to investigate evidence that linked him to the killing within months of the murder.

In court papers, Ms. Angeli notes that Sobel was quizzed about the murder several times between December 1989 and July 25, 1990, and that, in that same period, he was fingered by a participant in the slaying.

By ignoring these leads for 16 years, Ms. Angeli argues, prosecutors made it difficult for Sobel, now a commercial fisherman in Florida, to prepare a defense. The delay violated his right to a speedy trial and mandates that the indictment be dismissed, she wrote.

The hearing, which began earlier this month, resumes next week before a New York Supreme Court justice, Gustin Reichbach, in Brooklyn.

Meanwhile, sources said that the office of District Attorney Charles Hynes, which had filed a notice that it plans to appeal Judge Reichbach’s dismissal of the Sinagra indictment, has decided an appeal would be fruitless and will forego that option. Instead, it will focus its efforts on Sobel’s ongoing pretrial hearing and a subsequent one in the case of Mr. DeVecchio that is slated for August.

A spokesman for the Mr. Hynes’s office declined to comment about the district attorney’s current intentions in the Sinagra case.

This column and other news of organized crime will be available today at ganglandnews.com.