The two got into an argument outside a B6 bus near Bay Parkway and East 2ndStreet just before 9:40 p.m.
The victim appeared to be holding onto the bus as he biked alongside it.
Police said the 42-year-old bus driver, Michael Brown, got out to address the teen and an argument culminated in him punching the 16-year-old several times.
The teen was taken to the hospital to be treated, possibly for a broken nose.
Brown is facing a slew of charges including assault, reckless endangerment and acting in a manner injurious to a child under 17.
MTA Communications Director Tim Minton released a statement Tuesday that said, "This matter remains under investigation. Preliminary reports indicate the cyclist was endangering passengers by engaging in reckless behavior before escalating the situation.All facts should be considered."
The Transport Workers Union Local 100 said in a statement:
"Last night a male cyclist was hanging onto a bus as it was being driven. The operator saw the cyclist in the mirror and stopped the bus. When the operator addressed the cyclist about the unsafe condition, the situation escalated. The incident is still under investigation."
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