A young woman was shot in a Coney Island bodega yesterday, while two children were standing by her side, authorities said.

The 24-year-old victim was shopping at the Seabreeze Deli on Neptune Avenue near West 36th Street with her 3- and 6-year-old nieces when a gun-toting thug came in and fired off three rounds at 3:15 p.m.

The thug, who was apparently aiming for a man standing close to her, missed and struck the victim twice, once in the back and once in the arm, sources said.

The children were unharmed. Their aunt was in stable condition at Lutheran Hospital.

No arrests have been made, police said.