The two were shot at approximately 2 p.m. local time (1800GMT) near the Al-Furqan Jame Masjid Mosque in Ozone Park while walking home from prayers.
The imam, identified by police as Maulama Akonjee, 55, was reportedly shot in the head as was his companion, an unidentified 64-year-old male.
Witnesses told police the male suspect fled the scene with a gun in his hand, New York Police Department Deputy Inspector Henry Sautner said.
The suspect remains at large and Sautner said no motive has yet been established.
A local resident told the New York Post newspaper that it appeared the gunman picked his targets before fleeing the scene on foot.
“There was a carload of people across the street, and a girl across the street, and he just targeted these two guys,” the resident said.
NBC4 New York reported that a preliminary investigation indicated that the men were shot during the course of a robbery, but added that authorities said they may have been targeted.
Afaf Nasher, executive director of the New York chapter of the Council of American-Islamic Relations said in a statement that the perpetrator “must be swiftly apprehended and face the full force of the law.”