Jay Bryant, 49, is currently being held on unrelated federal drug charges and will be arraigned on the murder charge at a later date.
An email seeking comment was sent to Bryant's attorney.
Karl Jordan and Ronald Washington were previously charged with the killing of Jason Mizell, also known as Jam Master Jay, at a recording studio in Queens on October 30, 2002.
No death penalty for accused Jam Master Jay killers
The hip-hop trailblazer was shot in the head.
At the time the other two men were indicted, authorities said Jay's death involved a drug deal gone bad. In a letter filed with the court on Tuesday, prosecutors said Bryant and the two other men entered the building that evening, and then fled after the shooting. They said Bryant was seen going into the building, and his DNA was recovered at the scene.
Jay was in Run-DMC with Joseph "Run" Simmons and Darryl "DMC" McDaniel in the early 1980s. The group helped bring hip-hop music into the mainstream. Run DMC's hits include "King of Rock," "It's Tricky" and a remake of Aerosmith's "Walk This Way."
For years, Jay's death lingered as a cold case, with witnesses reluctant to speak up despite reward money being offered.
The Associated Press contributed to this report.