The boat, a 31 foot Contender, crashed into the bulkhead of a waterfront property of a Crystal Beach Boulevard home just after 5:30 a.m.
Two of the three men on board were tossed into the water.
One of them, a 57 year old from Southampton, stayed on the boat. He sustained the most serious injury, to his back. He was taken to Brookhaven Memorial Hospital, along with a 41 year old from Center Moriches.
A third man, a 36 year old also from Center Moriches, declined treatment at the scene.
The 41 year old operator of the boat apparently lost control lost in the area of Old Neck Creek.
The cause of the crash is under investigation. Alcohol does not appear to be a factor.