Crowe, 41, who plays a boxer in his latest film, "Cinderella Man," threw the phone at the Mercer Hotel employee, striking him in the face, during an argument at around 4:20 a.m., said police spokesman Sgt. Mike Wysokowski.
The Australian movie star was taken into custody, fingerprinted and charged with second-degree assault, said police Lieutenant Eugene Whyte.
Crowe was expected to appear in Manhattan Criminal Court later Monday.
No one at the Mercer Hotel would talk about the incident, reports Sean Adams of radio station WCBS-AM.
An employee at the hotel in SoHo who answered a call from the Associated Press said he was unaware of the incident.
Crowe won an Oscar for his role in 2000's "Gladiator."
"Cinderella Man," Ron Howard's story of Depression-era boxer Jim Braddock, had a lackluster opening this weekend, debuting at No. 4 with an estimated $18.6 million at the box office.
Universal had counted on a better debut for the film, which reunites Howard, Crowe and producer Brian Grazer, the team behind the 2001 Academy Awards champion "A Beautiful Mind."