Gotti, 45, who insists he left organized crime a decade ago, has been free on $2 million bail since a jury deadlocked on Dec. 1 after deliberating for 11 days, forcing a mistrial. He spent the holidays at home on Long Island with his family.
Three trials in 2005 and 2006 also had ended in hung juries.
Those prosecutions began as Gotti was completing a five-year sentence he received after pleading guilty in 1999 to federal charges over the objections of his father.
The repeated hung juries left some comparing Gotti to his late father, John Sr. The elder Gotti escaped conviction in a series of trials in the 1980s and early 1990s, gaining him the nickname "Teflon Don" because the charges wouldn't stick to him. Also known as the "Dapper Don" for his stylish suits, Gotti was, for several years, the most notorious mobster in the United States.
The senior Gotti was finally convicted of racketeering in 1992 and sentenced to life in prison. He died in prison in 2002.
The younger Gotti was accused of ordering a kidnapping and attempted murder plot against Curtis Sliwa, founder of an anti-crime group called the Guardian Angels who had criticized Gotti Sr. on his radio talk show. Sliwa was first beaten with a baseball bat in 1992 and was later kidnapped, shot and nearly killed.
Federal prosecutors in Tampa, Fla., brought the latest case in 2008, but it was returned to Manhattan by a judge who said he was left with the "unmistakable and disquieting impression" that the government had shopped for a trial location where it might finally win.
Prosecutors for the first time also attempted to tie Gotti to multiple murders, in addition to the claims about Sliwa.
Seth Ginsberg, one of Gotti's lawyers, called the move to drop the case the "right decision" and added, "I hope that they stick to it this time and let John and his family be at peace."
Junior Gotti's latest trial was punctuated by outbursts by Gotti's mother and once by Gotti. At one point, Gotti shouted to John Alite, the star prosecution witness: "You're a punk! You're a dog! You're a dog! You always were a dog your whole life, you punk dog."
Gotti's mother, Victoria, screamed out to her son once when the jury was not in the room: "They're railroading you! They're doing to you what they did to your father!"
