It happened at 353 83rd St. just before 3:45 a.m.
The crash also damaged an outdoor dining structure.
Police say the driver of the M15 bus blew multiple red lights as she headed northbound on First Avenue before crashing.
Authorities are looking into whether she fell asleep before the crash.
A passenger was also on the bus at the time, but neither the passenger or the driver were injured.
The driver was taken to the hospital to be checked out.
The MTA said in a statement that the bus operator is being withheld from duty pending an NYPD and MTA internal review.
Few other details were released.
----------
* Get Eyewitness News Delivered
* More Manhattan news
* Send us a news tip
* Download the abc7NY app for breaking news alerts on the go
* Download our connected TV app