The men were approached from behind by a man who shot them both in the head, a police spokesman said.
Imam Maulama Akonjee, 55, moved to the city from Bangladesh two years ago, US media reported.
Some mosque-goers said they believed it was a hate crime but police said there was as yet no evidence that the men were targeted because of their faith.
A man holding a gun was seen leaving the scene of the shooting in the Ozone Park area, but no-one has been arrested.
Police said the suspect had a "medium complexion". They released a sketch on Sunday.
Imam Akonjee and his assistant Thara Uddin, 64, were shot a short walk from the al-Furqan Jame mosque at about 13:50 local time (17:50 GMT) on Saturday.
Okay let's be honest, i'm not surprised that this news thread hasn't been made here. Because i read this about this on my local news outlets hours ago.
But RIP to the Imam and his assistant. I heard this makes some muslims who live there are afraid bout their life
Disgusting. Why do people not realise that Islam is a religion of peace? These men had done nothing to harm anyone.
Muslims may be peaceful. Islam itself, however, is not All the Abrahamic religions promote violence and discrimination in their holy books - especially Islam.
Violence is never the answer, regardless of how you feel about Islam / religion in general.
All the Abrahamic religions promote violence and discrimination in their holy books - especially Islam.