The crime, among the largest cash heists in US history, was dramatized in the 1990 movie Goodfellas.
Vincent Asaro and four other alleged mobsters were charged with crimes dating as far back as 1968 – murder, arson, extortion, robbery and more.
The men are expected to appear in court on Thursday afternoon.
On December 11, 1978, hooded gunmen rushed into Lufthansa Airlines’ cargo terminal at New York’s JFK airport and stole $5 million being transported to a Manhattan Bank from West Germany, as well as $1 million in jewellery.
Investigators said the thieves were familiar with the cargo building’s layout, including the location of the high-value storage room, and addressed several Lufthansa employees by name.
The cash was never found.
Vincent Asaro, an allegedly high-ranking member of the Bonanno crime family, was arrested on Thursday and charged in federal court in New York with the robbery.
He is also charged with a 1969 murder, extortion and illegal gambling.
The indictment charges him and Jerome Asaro, accused of being a “captain” in the Bonanno family, with the theft of $1.25 million in gold salts from Federal Express, a US freight service.
Vincent Asaro and Jack Bonventre, another alleged Bonanno associate, are charged with illegal gambling.
In addition, the Asaros, Thomas DiFiore and John Ragano are charged with a litany of crimes between them including racketeering, extortion, arson and murder solicitation.
The authorities have had difficulty bringing charges in the case over the years, largely because so many people suspected of involvement in the heist were killed by nervous mobsters.
Just two years after the robbery, The New York Times reported at least six murder victims were believed to have been connected with the case.
A cargo agent for the airline with gambling debts was the only person ever convicted in connection to the crime.
In June, FBI investigators descended on a neighborhood in the New York borough of Queens where they believed the robbery was planned.
The agency believed James Burke, a now-deceased Lucchese crime family associate who inspired Robert De Niro’s character in Goodfellas, masterminded the heist.
Investigators used jackhammers and shovels to dig beneath James Burke’s house.
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