Daniel Barrera Barrera, 44, faces a mandatory minimum of 10 years in prison or a maximum of life in prison if he is convicted. He also faces charges in federal court in Miami, where he would be taken after the court cases are completed in New York.
Barrera was designated in March 2010 by the U.S. Treasury Department as a special designated narcotics trafficker. He was arrested last September in Venezuela. He was then sent to Colombia, where the U.S. pursued his extradition.
Colombian President Juan Manuel Santos has called Barrera "the last of the great capos." He is known to authorities in Colombia as "El Loco."
U.S. Attorney Preet Bharara said in a release that Barrera's organization produced as much as 400 tons of cocaine annually and used some of the proceeds to fund terrorist groups, including the Revolutionary Armed Forces of Colombia or the FARC.
Authorities said he purchased raw cocaine base or paste from the FARC and converted it into powder at laboratories he owned and operated in an area of Colombia once controlled by the since-demobilized terrorist group, Autodefensas Unidas de Colombia or AUC.
James Dinkins, executive assistant director of the U.S. Immigration and Customs Enforcement's "ICE" Homeland Security Investigations, said Barrera and his co-conspirators are accused of running one of the largest cocaine trafficking operations in history.
U.S. Attorney Loretta E. Lynch in Brooklyn, where Barrera also is facing charges, called Barrera "the kingpin of a stunningly prolific Colombian drug cartel, which flooded the globe with its deadly product."
She said the money he provided terrorist organizations in Colombia was "responsible for decades of death and destruction in Colombia, all to ensure his deadly business ran smoothly."
New York Police Commissioner Raymond Kelly said: "If any one case epitomizes the nexus between terrorism and drug trafficking and the destructive impact on Colombian society, this is it; not to mention the crime and suffering cocaine addiction has fueled on the demand-side of the equation in the streets of New York."
Authorities also said Barrera laundered tens of millions of dollars of profits as he processed about 30,000 kilograms of raw cocaine into the same amount of cocaine powder each month since 1998.
He has had several cosmetic surgeries and tried to burn off his fingerprints with acid to mask his identity, authorities said. Venezuelan officials say they confiscated houses, ranches, a yacht, apartments and 48 cars from Barrera.