The woman was found by her two young daughters, ages 15 and 5, inside their Chauncey Street apartment in Brownsville just before 9 p.m. Wednesday.
A memorial has been set up outside the building to remember 46-year-old Sellis Gonzales, who lived on the second floor.
Police have identified the suspect as 40-year-old Erik McCormick, who is the father of the 5-year-old girl.
Authorities say he showed up at the home around 8 p.m. Wednesday and gave the girls money to buy fried chicken at a restaurant around the corner.
When they returned, NYPD Commissioner Ray Kelly said, they found the door ajar and their mother in a pool of blood, shot six times. Gonzalez was reportedly shot three times in the head and three times in the chest.
She was rushed to Brookdale Hospital, where she was pronounced dead on arrival.
McCormick is described as a black male, 5-foot-8 and weighing 225 pounds.
Anyone with information in regards to whereabouts of Eric McCormick is asked to call the NYPD's Crime Stoppers Hotline at 800-577-TIPS.