Authorities say 59-year-old John Mirabito was arrested in Glen Cove after the incident, which occurred around 8 a.m. Monday on the Long Island Sound.
Investigators say Mirabito, who was clamming at the time, crashed his boat into another clamming boat and then began arguing with the driver.
That's when they say Mirabito took a rifle out of his cabin and pointed it at the other man.
The boater started his engine and fled the scene, then called police. Mirabito was arrested a short time later, and the rifle was apparently recovered inside the cabin.
No injuries were reported.
Mirabito is charged with two counts of second-degree menacing.