The airline is "incredibly saddened" and focusing on the pilot`s family and colleagues, a spokeswoman said.
Flight 550 left Phoenix before midnight on Sunday and landed on Monday morning.
The pilot appeared ill during the flight, prompting the diversion, said Michelle Mohr, the spokeswoman.
A new crew was sent to Syracuse to fly the passengers to Boston, where they arrived on Monday early afternoon.
There was never a question about whether the flight would be able to land safely, said Ms Mohr.
"We`re certainly well qualified to handle situations like these," she said. "That`s why you`ve got more than one pilot in a cockpit."
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