Salvatore Perrone, 63, of Staten Island, had tried to sell clothing to the shopkeepers, New York City Police Commissioner Raymond Kelly said.
According to CBS New York, detectives had been questioning Perrone for almost 24 hours after he turned himself in on Tuesday.
Earlier this week police said they were looking to speak to four people who possibly witnessed the most recent killing last Friday, and released video and clear images of all four. But they zeroed in on a man with a duffle bag seen in surveillance video. That man, dubbed "John Doe Duffle Bag," they now say was Perrone.
Police recovered a bag containing a sawed-off rifle believed to have been used in the killings.
Police Wednesday were outside the Midwood apartment building where Perrone's girlfriend, Russian immigrant Natasha Charova, lives. Sources said Perrone stashed the duffle bag at her place, and that they.found a .22 caliber gun inside, CBS New York reported.
The station cited sources who said the bag also contained women's stockings, black gloves, a laser scope and two knives. One of the knives had stains that appeared to be blood, 1010 WINS Radio reported.
In the most recent killing last Friday, Rahmatollah Vahidipour, an Iranian, was shot three times in the head and chest at his store, the She She Boutique.
After that killing, detectives discovered the same gun was used in the fatal shootings of two other shopkeepers when ballistics matched the .22-caliber gun shell casings on all three. On July 6, Mohamed Gebeli, an Egyptian, was found shot in the back of his shop, Valentino Fashion Inc. On Aug. 2, Isaac Kadare, also Egyptian, was shot in the head in his store, Amazing 99 Cent Deal.
There were other similarities, authorities said: The bodies were all partially obscured, by clothing or, in one case, a box. The locations of the shops form an equilateral triangle and are about 4 miles apart, with addresses that contain the number eight. Money was taken from everyone but Vahidipour, who had $171 in his pocket.
CBS New York reported that Perrone was previously arrested in 2001 in Pennsylvania, where he was accused of burglary and stalking an ex-girlfriend.