The rapper is known for hits including Fefe with Nicki Minaj, and Stoopid, featuring Bobby Shmurda, who is currently in prison.
The "violent" defendant was deemed a likely danger to the community and denied bail after a prosecutor told a court there was evidence he directed or participated in multiple acts of violence as part of a gang.
Assistant US attorney Michael Longyear said a backpack stolen during a gunpoint robbery in April was found during a raid at the 22-year-old's home in Brooklyn, along with an automatic pistol.
He also said 6ix9ine was captured on surveillance video as he sat in a car and filmed the scene in Times Square, where his co-defendants allegedly carried out a violent robbery against a rival gang member.
"The defendant is quite violent," the prosecutor said.
The rapper has worldwide connections and hundreds of thousands of dollars and therefore poses a flight risk, Mr Longyear told the court.
He is also aware that a conviction would bring a mandatory minimum sentence of 32 years in prison and as much as life, the prosecutor said.
Judge Henry B Pitman ordered the rapper to be held until a bail hearing.
6ix9ine was among five people charged in an indictment containing racketeering and firearms charges.
His lawyer, Lance Lazzaro, said the rapper - real name Daniel Hernandez - poses no threat and denies directing or playing any other role in violence.
Mr Lazzaro said his client had fired some of his co-defendants as part of his management and security team last week.
6ix9ine has seen a huge rise to fame and has become one of the most controversial names in hip-hop.