The Q20 bus collided with the Dahlia charter bus at Main Street and Northern Boulevard in Flushing around 6:15 a.m., and authorities were investigating reports that the charter bus had run a red light.
The NYPD and FDNY responded to the scene and began removing passengers.
"It was bad, it was really bad," witness Mike Ramos said. "I felt the vibrations shake my truck...I saw a guy with a cracked head, a cracked skull open. I saw guys bleeding all over the place...When I ran across the street, there was a woman pinned, screaming in the back of the city bus. I guess she was one of the pedestrians walking on the sidewalk."
PHOTOS: Scene of deadly bus crash in Queens
All of the victims were quickly taken off the buses, with the exception of one of the drivers, who was pinned in the bus and needed to be extricated. One person was pronounced dead at the scene after being found underneath one of the buses, leading authorities to believe that person may have been a pedestrian.
The victims were rushed to area hospitals, where two of them passed away and five remain listed in critical condition. The driver of the private bus and a passenger on the MTA bus were identified as those who died at the hospital.
The MTA driver, a 10-year veteran, "is in the hospital in non-critical condition, he's being spoken to," authorities said.
The force of the collision sent the charter bus onto the sidewalk and into a Kennedy Fried Chicken, sparking a small fire. The flames were quickly extinguished, but there is extensive damage to the structure.
The cause of the crash is under investigation, but one witness who was in a car that was nearly struck by the charter bus said it was speeding and ran several lights.
"I looked up, and I see this bus fly right by us," Sheila Baez said. "He flew, we was at the red light, he flew right by us. He passed the red light...speeding. He went past the red light, he went passed the other red light, and smacked into the bus. He hit the bus...He ended up on the sidewalk, then smacked into the building. That's what we saw."
New York City Mayor Bill de Blasio visited the accident scene, calling it "a really tragic morning here in Queens."
"It's hard to compare it to anything I've ever seen, the sheer destruction from the impact of this collision," de Blasio said.
WATCH: Mayor de Blasio speaks after visiting crash site
The NTSB is sending team to New York City to investigate the crash.
Another Dahlia charter bus was involved in a 2016 bus crash on Interstate 95 in Connecticut that killed one and injured 36.
In that incident, the driver lost control on the snow-covered highway, skidded off the road and rolled over. The bus was being operated by VMC East Coast at the time. It appears the company that owns the buses was most recently flagged by Federal DOT for a high number of safety violations, including 10 in the last 24 months for speeding. It's not clear if the bus in Monday's incident was being leased by another operator.