A judge continued bail for both men at $5 million each. They are each charged with five counts of murder and one count of arson.
Investigators have called this the most baffling case in Newark's entire history.
Almost 32 years ago, Lee Evans was the prime suspect when the five teenagers vanished in 1978.
The teens were with Evans, a carpenter, who routinely hired teens to help him with odd jobs, police have said.
Evans was repeatedly interviewed and passed a polygraph test, eventually cleared as a suspect, until now.
Evans and Hampton, were also charged with arson. Officials say they put the boys in a home and burned it to the ground.
Investigators say that on August 20, 1978, 16-year-old Randy Johnson, 16-year-old Michael McDowell, 17-year-old Melvin Pittman, 16-year-old Alvin Turner and 17-year-old Ernest Taylor vanished after playing basketball.
"With these arrests today, we hope to bring closure to a 31-year-old mystery involving five teenage boys who vanished from Newark on Aug. 20, 1978,'' said Acting Essex County Prosecutor Robert Laurino. "For years their families wondered what happened on that August day. Today, we believe, that question has been answered.''
The Essex County prosecutor's office said Tuesday a tip from a witness 18 months ago led to the arrests.
Evans told police at the time that he dropped off the boys on a street corner near an ice cream parlor. Later that night, Michael McDowell returned home and changed clothes, then returned to a waiting pickup truck with at least one other boy inside. That was the last confirmed sighting of any of the teens.
Evans and a second suspect were tightlipped Monday night as they were led out of the Essex County courthouse in handcuffs.
A third man believed to have been involved died two years ago.
Police believe the boys had broken into one of the suspects' apartments and stole marijuana.
Newark Police Director Garry McCarthy expressed his condolences to the family and loved ones of the victims who have endured decades of immeasurable pain coping with the uncertainty surrounding the teens' disappearance.
"I hope that the relentless pursuit of justice demonstrated by the investigators on this case will bring some level of solace to the families,'' McCarthy said.
Acting Prosecutor Laurino praised the investigative team for its extraordinary detective work in bringing this investigation to a close.
"The arrest and charging of the two suspects in this case represents the beginning of the final chapter in the most heinous crime ever perpetrated not only in the city of Newark, but the state of New Jersey,'' said Col. Fuentes. "The investigative partnership between local, state, and county law enforcement was paramount in assuring that the victims and their families were never forgotten and this case was solved.''
(The Associated Press contributed to this story.)