The three-story transit hub features an atrium that allows natural light to reach the subway station and the below-ground LIRR concourse.
Some 57,000 riders come through the station daily.
The neighboring 22-acre Atlantic Yards project would include a new arena for the New Jersey Nets. The pavilion would better accommodate a surge in riders for the arena.
The heads of the LIRR and Metropolitan Transportation Authority attended Tuesday's ceremony.
The old terminal opened in 1907 and closed about 20 years ago.
