Officers took the suspect into custody on an unrelated warrant.
The shooting happened last Saturday during a robbery at the Lucky Grocery & Deli in Laurelton.
Juan Torres, 54, was killed. Police believe he tried to sneak up on the suspect, who was robbing Torres' brother Felix inside the deli.
The deli was the scene of another murder just a few years ago, in which a Torres family friend who worked at the deli was shot and killed. Also, Torres' older brother Jesus was murdered during a deli robbery in Brooklyn a decade ago.