Police say the 30-year-old burglar was confronted after breaking into the home on East 64th Street just before 2 a.m. Wednesday.
The 62-year-old homeowner shot the burglar three times.
The suspect was hit twice in the torso and once in the arm. He was rushed to Brookdale University Hospital in critical condition.
The homeowner had a pistol license for his weapon.
The suspect is under arrest at the hospital. Charges are pending.
Police were investigating if a second suspect fled the scene.