A horrific collision between a private tour bus and an MTA bus in Queens left three people dead — including the tour bus driver — and 16 injured early Monday, authorities said.

Firefighters and first responders swarmed the scene following the deadly 6:20 a.m. crash in Flushing at the intersection of Northern Boulevard and Main Street, using hydraulic extrication devices to free some of those trapped in the wrecked buses.

The city Q20 bus holding 15 passengers was making a right turn onto Northern Boulevard from Main Street when it was struck by the private bus, which traveling eastbound on Northern Boulevard. That caused the city bus to flip around, officials said.

The private bus, run by the Flushing-based Dahlia Travel and Tours,then crashed into a Kennedy Pizza & Chicken – causing substantial damage to the building and igniting a small fire inside — while the MTA bus was smashed up against it, facing the wrong direction on Northern Boulevard, officials said.

Two of the three fatalities — the tour bus driver and an MTA bus passenger — died at area hospitals, while a pedestrian on the sidewalk, who became pinned under one of the buses, was killed at the scene, according to officials.

Of the 16 people injured, five were in critical condition “and fighting for their life right now,” Mayor Bill de Blasio said at a press conference.

The others hurt — including the MTA bus driver, who has 10 years on the job — suffered non-life-threatening injuries and were listed in stable condition.

Emergency responders rushed the injured to New York Hospital Queens and Elmhurst Hospital, officials said.

Among the injured was Kang San, 56, who had stopped to get coffee at a nearby shop and was sitting in his Toyota on Northern Boulevard when his car was struck during the collision.

“My husband is lucky. Maybe two minutes [earlier] it would be worse. He was walking before,” said San’s wife, Yung Lim, 62, who noted that San was picking up his co-workers. “He said, ‘I am lucky today.’”

San was taken to Elmhurst Hospital after suffering injuries to his back and leg, Lim said.

“He was nervous,” Lim said at the scene, adding, “When I come here, a lot of people lying on the floor. A lot of people were in pain.”

Queens resident Yong Suk Miller, 66, heard the crash from inside her seventh-floor apartment on Northern Boulevard.

“I feel the building shake a little. I hear crunching and shaking,” Miller said. “I thought it was truck. Then I hear a lot of ambulances and fire trucks. This is bad.”

A passer-by said he thought the incident was related to terrorism.

“I was just coming from work. I thought it was a terrorist attack, I saw so many sirens and lights flashing,” Jay Rivera, 52, told The Post.

“I’ve never seen an accident of this magnitude. The impact must’ve spun the bus around. A lady told me that the buses hit at full speed. They have the Jaws of Life out, so you know it must be bad,” he said.

Investigators are canvassing the area for surveillance video.

A person who answered the phone at Dahlia said he didn’t know about the crash and hung up.

The collision snarled traffic and caused heavy delays.