Also on Tuesday, Somali pirates freed a chemical tanker and its 23 Filipino crew members after holding them hostage for more than five months.
The ship had reportedly been carrying a cargo of phosphoric acid from Dakar, Senegal, and was en route to Kandla in India with its crew when it was seized.
It is not clear if a ransom was paid.
Muse arrived in New York on Monday night surrounded by US federal agency and smiling despite being handcuffed with a chain wrapped around his waist. He also had a heavily bandaged arm - reportedly from a wound sustained during the skirmish on the cargo ship.
He will reportedly be charged under two federal laws that deal with piracy and hostage-taking, an official told AP, the first such US piracy charges in more than a century.
|Concerns over piracy in the shipping lane
off the Horn of Africa have grown [EPA]
The hostage charges relate to the pirates seizing Richard Phillips, the US captain of the Maersk Alabama, and holding him hostage in a small lifeboat.
Phillips was later rescued by US forces after navy snipers shot dead three of the pirates and seized Muse, allegedly as he was negotiating over the captain's release on a US vessel.
Teenage defendants are entitled to greater protections under international law, and Muse's age could factor into a prison sentence if he is convicted.
The government has not said how why it considers the defendant to be 18, but verifying his actual age could prove difficult because the lack of records and stability in Somalia.
Plea to Obama
Muse's mother said on Tuesday that he had been coerced into piracy by "gangsters with money" and appealed to Barack Obama, the US president, to release him or to allow for her to visit where he is being held.
"I appeal to the American government, President Obama to release my young, poor misled 16 year old student son. I appeal for his release. If not, I ask him to take me to where he will be tried," Adar Abdirahman Hassan, who lives in the Somali town of Galkayo, told the AP news agency.
The boy's father, Abdiqadir Muse, also said the pirates had lied to his son, telling him they were going to get money.
The hijacking of the Maersk Alabama prompted calls for tightened measures to protect US ships in the busy shipping lanes off Somalia, where a transitional government is aiming to assert authority over the country after opposition fighters took control over the southern and central regions.
Muhdin Mohamad Ali, from the Centre for Somali Policy, a London-based think tank, told Al Jazeera that piracy should not be the main focus when it comes to Somalia's continuing crisis.
"There has been no functioning government for nearly two decades, and numerous attempts to form governments have not worked or contributed to stabilising the country. Piracy is merely a symptom of this situation," he said.
Ali also said that while millions of dollars in aid is being pledged at an international conference on Somalia in Brussels, "the pouring of money into a failed state will not work unless concerted efforts are made to reach out to all factions inside the country".