A man and a woman walked into the store when suddenly one of them pulled out a gun and jumped over the counter, police said.
The owner of the store then pulled out his own gun and a gunfight broke out.
The owner was able to hold one of the suspects on the ground until police arrived even though he was hit by a bullet during the attempted robbery.
Police led the woman away in handcuffs.
The window of the store was shattered by the gunfire. Police said they don't even know how many shots were fired inside the store.
"The owner and the suspects are very fortunate to be alive right now," said Det. Sgt. John Giambrone.
As police dogs searched for the gun, which still has not been found, friends of the owner said he knew the store was vulnerable.
"He said it happened to him a couple of years ago," said Kenny Collins. "What can you do? It's Christmas time. You let people in. He has a buzzer and buzzes people in. It didn't work out tonight."
Investigators said the owner was shot in the chest during the confrontation. He was taken to South Nassau Hospital, where he was listed in stable condition.
Police launched a manhunt for two other suspects after the robbery.
At one point, investigators were stopping LIRR trains in search of them.
They caught a second suspect near the shooting scene.
The third person remained at large late Wednesday night.