The incident happened during a brazen robbery in Greenpoint that was caught on surveillance video.
Police say Felix Lagoa was identified from fingerprints left during the July 25 robbery of Studio Jewelry. He was arrested Saturday at his home.
"I'm f---ed," Lagoa was quoted by prosecutors as saying. "I guess I'll cop a plea, but I'm not snitching."
Lagoa was charged with attempted murder, assault, robbery, grand larceny and criminal possession of a weapon.
His accomplice, who was caught on camera snatching $50,000 in jewelry from the display case, remains on the loose.
The store owner, 54-year-old Richard Sanocki, was shot in the stomach and remains in a medically-induced coma. His spleen was removed, according to prosecutors.