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 injured have been sent to three nearby hospitals, Officer James Byrne with the New York Police Department (NYPD) said.
The driver of the MTA bus is hospitalized with non-critical injuries, officials said. The charter bus driver and a passenger on the city bus also were killed.
"These buses spun around", MTA Chairman Joe Lhota said at the news conference.
The mayor cautioned that it is still too early to know if anyone was at fault and that the cause of the crash is under investigation. "That requires an enormouse amount of speed". Sixteen other people were hurt, some of them seriously, in the crash at 6:15 a.m.in the Flushing, Queens neighborhood, city officials said at a briefing. "It's hard to compare it to anything I've ever seen, the sheer destruction".
The NYPD said to avoid the area. "We want to make sure we understand exactly what happened, and we prevent this from ever happening again".
A representative for Dahlia Travel and Tours could not immediately be reached for comment.
Federal regulators have cited Dahlia for unsafe driving in the past.