Sixteen-year-old Justin Casquejo, of Weehawken, was arrested after his stunt on March 16.
Police say he managed to squeeze through a 1-foot by 1-foot hole in the fence that surrounds the property and made it past security on his way to the spire.
He now faces jail time.
On Wednesday, prosecutors added a BASE jumping charge, related to his climbing a building or hanging from a building.
The new charge is the most serious one Casquejo now faces, an class A misdemeanor, which could be punishable by up to one year in jail. The other charges are class B misdemeanors.
He allegedly broke into the building around 4 a.m. on a Sunday with no identification and apparently dressed like a construction worker.
The teen apparently had little trouble getting past security. He was stopped by another construction worker who spotted the red light on his GoPro camera as he attempted to leave the building, and police were called.
"We take security and these types of infractions extremely seriously and will prosecute violators," Port Authority Chief Joseph Dunne said. "We continue to reassess our security posture at the site and are constantly working to make this site as secure as possible."
Casquejo was detained by Port Authority police officers responding to a report of a unauthorized person on the site.
Casquejo was in possession of a camera and a cell phone and had apparently taken pictures from the top of the building, where he stayed for about two hours.
Port Authority officials said the breach and security at the site are all under investigation.Casquejo released an apology on his twitter feed, saying, "I seriously apologize to anyone who may have been insulted or felt disrespected by my actions. It was not my intention to do so."
Prosecutors say in the indictment that "the defendant jumped and attempted to jump" from the building, "climbed and attempted to climb up, down and around" the building "and suspended and attempted to suspend" from the exterior of the building on March 16.
Prosecutors requested Casquejo be assessed in a program for youthful offenders, making jail time less likely.
He was ordered to return to court April 30. He was ordered to return to court April 30.