FDNY Marine 6 and an NYPD Harbor Unit came to the rescue of the boaters.
The 25 foot Grady White overturned just after 8 a.m. on Saturday morning.
The boat was a safety boat that was patrolling the waters for racers in the Liberty Challenge that takes place in Manhattan every year.
"The current was pretty rapid going north, so one of the people in the water was moving pretty quickly, but we got them out," said Chief Jim Hodgens with the FDNY.
The boat was secured and tied to the Manhattan Bridge as the investigation continued.
Two victims were taken to Belelvue Hospital to be evaluated and one person was treated at the scene.