David W. Banach, who claimed he was looking at stars with his daughter, also was accused of lying to the FBI about the Dec. 29 incident in which the jet's windshield and cabin were hit three times with a beam as the plane approached Teterboro Airport.
The charges in the federal indictment were similar to those filed against Banach in an FBI complaint in January; the indictment replaces the complaint.
Attorney Gina Mendola-Longarzo said Banach was using the laser for stargazing when the plane was hit by the beam.
''I think it's an absolute abuse of prosecutorial discretion to charge my client under the Patriot Act for non-purposeful conduct,'' she said.
U.S. Attorney Christopher J. Christie said in a statement officials took the actions ''very seriously, and we will not condone lying to federal agents.''
Banach, 38, faces up to 20 years in prison if convicted of interference with pilots of an aircraft ''with reckless disregard for the safety of human life,'' a provision of the USA Patriot Act passed following the Sept. 11 terrorist attacks.
He also was charged with two counts of making false statements to law officers, each of which carries up to five years.
