"The hotel had checked earlier in the morning at nine, and he was asleep, at one he was found dead," deputy commissioner Paul Browne told AFP, adding that Richard Descoings was found slumped "on his bed" by hotel staff.
Browne said the police were investigating, saying there was "no obvious sign of trauma" although "the room was in a state of disarray" due to efforts by medical staff to revive Descoings.
Browne later ruled out that the academic's death was due to an act of violent crime, saying "we haven't found evidence of criminality."
Descoings, 53, director of the prestigious Institute of Political Studies in Paris, was alone when he was found, Browne said.
His death comes 11 months after New York police were embroiled in the scandal surrounding prominent French politician Dominique Strauss-Kahn, who was accused of attempted rape by a maid in a Manhattan hotel. The charges were later dropped, but a civil suit is still pending.
Descoings died "on Tuesday in the middle of the day in New York," the prestigious French institute confirmed in a statement.
He had been attending a meeting of the heads of major universities under the aegis of UN Secretary General Ban Ki-moon, and had been due to meet four colleagues in the Michelangelo Hotel in Manhattan at 9 am.
When he failed to show up, they assumed he had left without them for the conference and only became alarmed when they could not find him.
A statement from the institute said Descoings had been at its helm for 16 years, during which he had "profoundly transformed" one of France's leading seats of learning, which traditionally educates the country's political and diplomatic elite.
French President Nicolas Sarkozy paid tribute to Descoings' "exceptional career," saying in a statement he had "devoted his whole life to his chosen cause... education."
French Foreign Minister Alain Juppé said France had lost "an indefatigable player in showcasing our country's higher education around the world.
"At this moment of great sadness, I pay tribute to the memory of a man of passion who never ceased in his commitment to equal access for all to knowledge," Juppé said.
Descoings was in New York to attend a Global Colloquium of University Presidents being held at Columbia University, at which Ban delivered the keynote address to the invitation-only meeting on Monday.
In a statement, Ban and Columbia University president Lee Bollinger paid tribute to Descoings, calling him "a global leader on education policy, recognized and honoured both in France and around the world for his contributions to research and policy."
During four consecutive terms, Descoings transformed the institution known affectionately as "Sciences-Po," increasing student numbers from 4,500 to 10,000 and ringing in huge changes.
He opened up the institute, one of France's "grandes ecoles," to poor families, set up six campuses in the provinces and widened intake to foreigners, who today make up 40 percent of the student body.
Known as a brilliant, inventive and at times provocative educator, Descoings championed "permanent innovation" and took part in many debates about opening up access to higher education in France.