Fellow teammate Antonio Pierce, who investigators said allegedly helped cover up the incident, was not charged.
The indictment comes nearly a week after the two men appeared in court to testify about the incident to a grand jury.
Burress is being charged with two counts of criminal possession of a weapon in the second degree and one count of reckless endangerment.
Other people involved in the case will likely not face charges, Manhattan District Attorney Robert Morgenthau said. He said others tied with the incident "showed first-degree bad judgment," but their actions did not amount to the level of a crime.
Burress was at the Latin Quarter nightclub the night of Nov. 29 when he inadvertently shot himself in the thigh after a gun tucked in the waist of his pants had slipped down his leg and fired. According to authorities, Pierce drove his then-teammate to the hospital and took the fire arm to Burress' home in Totowa, N.J.
According to police, the gun was not licensed and no one - including the players, NFL officials, or the hospital where Burress was treated - alerted authorities to report the gunshot wound, as required by law.
Burress faces up to three-and-half years behind bars. He pleaded not guilty to weapons charges earlier this year and is free on $100,000 bail. Additionally, he could face disciplinary action by NFL commissioner Roger Goodell under the league's personal conduct policy. Goodell's office announced in June that it had launched a probe into the shooting.
Burress, who was released from the Giants in April, has not yet been signed with another team.