The 22-year-old rapper, whose real name is Daniel Hernandez, was one of four people taken into custody Sunday.
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The arrests appear to be connected to a shooting at a party last month on the Upper East Side.
Among those arrested are the victim, Faheem "Crippy" Walter, who was shot during the fight, and Tekashi69's recently-fired former manager, 36-year-old Kifano "Shotti" Jordan. Jensel "Ish" Butler was also arrested.
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They are all charged with racketeering and firearms possession.
The rapper, also known as Tekashi 6ix9ine, has been one of the most ascendant and controversial names in hip-hop in recent months. His debut album, Day69, was among the most downloaded records on iTunes following its February release.
But he also has had a series of run-ins with law enforcement and has publicly identified himself as a member of a violent New York gang. He recently pleaded guilty to disorderly conduct in Brooklyn Criminal Court in connection with a May traffic stop.
In a 2015 case in New York, 6ix9ine was sentenced to probation for his involvement in a sexually explicit video of a 13-year-old girl.
The video, posted on social media, showed the girl performing a sex act on another man while 6ix9ine "stands behind the child making a thrusting motion with his pelvis and smacking her on her buttocks," according to court documents.
The shooting occurred outside what was a party to celebrate Tekashi69 receiving probation in that child sex case earlier in the day.