Authorities tell CBS News the pirate has been tentatively identified as 19-year-old Abdulwali Muse, and he is believed to be the group's ringleader.
Navy snipers shot his three cohorts as they held Capt. Phillips at gunpoint in a small boat off the stern of the USS Bainbridge, which had raced to the scene of the hijacked cargo ship.
Muse will face charges in New York's Southern District, which has experience handling cases against suspected terrorists.
It was this court that saw the convictions of Ramzi Yousef, the mastermind of the first bombing of the World Trade Center, blind Egyptian Sheik Abdel Rahman, and the co-conspirators in the 1998 African embassy bombings in Kenya and Tanzania which killed 258 people.
The official said it was not immediately clear when Muse would be brought to New York. The official spoke on condition of anonymity because he was not authorized to disclose information about the ongoing investigation.
The government had been weighing whether to bring the suspect to trial in the United States or hand him over to authorities in Kenya, which has an international agreement to prosecute pirates.
Since the hostage standoff in the Gulf of Aden ended on Sunday, U.S. authorities have been examining details of the case, particularly Muse's age.
Initially, he was thought to have been between 16 years and 20 years old, but Defense Secretary Robert Gates later said all four of the pirates involved were between the ages of 17 and 19.
If he is under 18, federal prosecutors must take a number of additional steps to justify charging him in federal court.
Though none have been filed publically yet, the suspect could face charges which carry a maximum sentence of life in prison.