In the largest ever case of its type in the city, the 103 young suspects face charges including conspiracy to commit murder, attempted murder and gang assault.
Manhattan district attorney Cyrus Vance said: "These three gangs were not sophisticated drug- trafficking organisations. Far from it, they were young people protecting their territories from imaginary threats and avenging the murders of fellow gang members and loved ones."
Forty suspects from three gangs were arrested in early morning raids in Harlem, 39 were already in jail over other offences and the rest are being sought by the authorities.
The crews warred over territory for two Harlem housing developments.