The incident occurred Monday night in Fort Lauderdale, Florida.
A witness said that passengers were already cranky when the JetBlue crew asked people who'd paid for extra legroom to switch seats because of weight and balance issues.
The 79-year-old Republican ex-senator was in a regular seat and led a chant, "Make them move."
Video shows D'Amato saying, "They're throwing me off the plane because I complained about what they were doing."
Check out the video here:
D'Amato's spokesman says he was sleep-deprived after visiting an ailing friend. Here's the full statement:
Anyone who knows Senator D'Amato knows he speaks his mind - but in this case he spoke after a long and demanding trip to Florida to visit an ailing friend, a five hour airport ground delay, additional delays as the crew sought to deal with weight and balance issues and then sleep deprivation. Jet Blue has apologized to the Senator for over reacting and the Senator apologized for speaking his mind at a time when he clearly had left his patience at the gate.
JetBlue says passengers can be removed if there's a situation that could escalate.
D'Amato represented New York from 1981 to 1999.
The Associated Press Contributed to this report.