The top of the bus was sheared off when it hit an overpass near Exit 19 in Lakeview just after 9 p.m.
Two victims, both 17-year-old females, were seriously injured and remain in the hospital. The driver and 43 other passengers on board were taken to several area hospitals, where they were treated and released.
"I think the entire incident could have been a whole lot worse," South Nassau Chief of Emergency Services Dr. Joshua Kugler said. "Fate has a lot to do with it. People, if they were standing on the bus at any particular time and someone became an airborne projectile, could have had a different outcome."
The commercial bus from Journey Bus Tours was traveling eastbound from JFK Airport. Authorities say 38 students from various Long Island schools, five chaperones, and one driver were returning from a trip to eastern Europe.
In a statement, the company told Eyewitness News, "We're not making any comments at the moment. Our greatest concern is for is for the passengers and their families."
Video showed teenagers sitting and standing outside of the white damaged bus, some draped in blankets, as firefighters inspected the wreckage. Multiple ambulances and firetrucks responded to the scene.
WARNING: Graphic language
Police say that driver, 43-year-old Troy Gaston, of Bethlehem, Pennsylvania, expressed remorse over the accident. He did possess a valid Pennsylvania commercial vehicle driver's license, but police said he was using a non-commercial GPS that may have played a factor.
"It was a stand-alone GPS that you would buy from a department store," New York State Police Major David C. Candelaria said.
The driver's planned GPS route was via the Belt and Southern State parkways. He did not have any alcohol in his system, investigators said. A drug evaluation is pending. Gaston did voluntarily provide a blood sample, police said.
State police will also conduct a comprehensive vehicle examination to rule out any mechanical issues. Being from out of the area, Gaston simply was not aware of the parkway system and the lower overpasses, police said.
New York State Police news conference:
"He made it all the way through," Cadelaria said. "We're very lucky. This could have been tragic."
The minimum clearance on the parkway is 7 feet, 10 inches, and accidents involving vehicles striking overpasses is not uncommon on the parkway. In 2017, there were reports that an electronic alarm system would be installed on the parkway to warn drivers of vehicles too high for the overpass.
The devices were recently installed near the site of the wreck but were still being tested, Department of Transportation spokesman Joseph Morrissey said.
"Safety is our top priority, and while we can't comment on an ongoing investigation, throughout this area there is signage indicating height restrictions and making clear that commercial vehicles are prohibited from driving on parkways," Morrissey said.
"If you're not from the area, you need to know how to maneuver around the area," one driver said. "I don't understand how he did not know, or he didn't measure it, or he didn't have a tour guide."
Many of the Suffolk County students attend Huntington High School. It was not a school-sanctioned field trip. In a statement, the superintendent expressed his thoughts and prayers:
"While injuries apparently ranged in severity, preliminary reports indicate that all have been treated and released, or remain under treatment. Our thoughts and prayers remain with all families involved. Student support staff remain on hand at Huntington High School for those in need."
The New York State Police are asking anyone who witnessed the collision to please contact 631-756-3300.
The Associated Press contributed to this report.