Authorities dealt a staggering blow to Long Island’s murderous MS-13 gang — busting 96 members and associates in the largest takedown of the notorious criminal group in New York state history, prosecutors announced Friday.

The arrests, all in Suffolk County, are the result of a nearly two-year county, state and federal investigation — and include nine cell, or “clique” leaders of the violent gang — virtually the gang’s entire presence in the county, officials said.

The investigation also thwarted seven Long Island-based murder plots, officials said.

And perhaps most importantly, the investigation prevented the El Salvador-based gang from getting a strong foothold on New York soil, according to Ray Donovan, special agent in charge of the DEA in New York.

“We’ve learned that through this investigation MS-13 had plans for establishing an East Coast foundation here in New York for the gang, that will never happen,” he said.

The bulk of the accused thugs, 64 defendants, were busted in the past week as part of a new indictment alleging murder conspiracy, drug trafficking, gang violence and the possession and sale of weapons, said Suffolk County District Attorney Timothy Sini.

“They’re decimated,” Sini said of his county’s estimated total of 10 cliques.

“They will attempt to recalibrate … and that’s why we need to stay vigilant.”

Nearly all of those arrested under the new indictment will be held without bail despite a lax new bail statute, because they’ve been hit with the non-bail-eligible charge of murder conspiracy, Sini said.

“Murder conspiracy, that’s not a bail eligible offense even under the new law, thank God,” Sini told reporters at an afternoon press conference that featured a table laid out with confiscated evidence, including 10 kilos of cocaine, 1,000 fentanyl pills, nine handguns, two long guns and numerous machetes.

“MS-13 is a ruthless, savage gang which commits acts of violence to recruit, retain and control its members and exact revenge on its rivals, as well as to extort innocent members of our communities,” Sini said.

Those newly indicted range in age from 16 to 59, and include illegal immigrants, US citizens, and non-citizens who are in the country legally, officials said.

They include nine leaders of “cliques,” or regional branches of the gang, who operated throughout Suffolk County and who officials say were sent to New York by the gang’s leadership in El Salvador.

They also include 19 of the gang’s alleged drug suppliers, officials said.

Portions of all drug sale proceeds would be sent back to those leaders in El Salvador, Sini said.

The clique leaders tried to impose a strict, El Salvador-mandated set of rules on members, including the often-ignored rule that gang members exhibit no vices.

“Their rules are very clear,” said Donovan.

“In order to move up from a ‘morro’ [rank] to a ‘chekeo,’ [higher rank], one would have to kill four times.

One Huntington-based clique required regular meetings — known as “masses,” — on the 13th of every month, Donovan said. Other rules stressed “zero drinking, zero stealing, zero violence, zero extortion, zero kidnapping,” he said.

But while management in El Salvador stressed that gang members should have no vices, “the reality is MS-13 has no rules,” Donovan said.

“Their rules are violence, fear, control of their territory.”

The FBI, the Drug Enforcement Administration, Homeland Security Investigation, the Bureau of Alcohol, Tobacco, Firearms and Explosives, the New York State Police, the Office of the Special Narcotics Prosecutor for the City of New York and the joined with Nassau and Suffolk County law enforcement and prosecutors in conducting the investigation and arrests.

The coordinated work of these law enforcement entities has contributed, in all, to more than 230 additional arrests in New York, throughout the US and in El Salvador the past two years, Sini said.

“This operation helped end the New York program, which was orchestrated by the leadership of MS 13 in El Salvador to develop a greater presence here on Long Island,” Sini said.

“Additionally as a result of the reliable intelligence generated throughout this investigation, law enforcement prevented countless acts of violence over the past 23 months, including seven murder plots right here in Suffolk County.”

The ruthless gang has been implicated in more than two dozen murders, including the brutal killings of Brentwood High School students Nisa Mickens, 15, and Kayla Cuevas, 16, in September 2016. The victims were hacked and beaten to death with machetes and baseball bats.

President Donald Trump has often cited the dangers of the MS-13 “infestation” to push for tougher immigration laws.

Additional reporting by Laura Italiano, Ruth Weissmann and Amanda Woods