Malik, whose lawyer said he was about to start a job as a drug counselor, was held without bail after his arraignment Tuesday on a murder charge.
Authorities said a passer-by found 28-year-old Betty Williams' body in a suitcase Wednesday in East Harlem.
A court complaint says Malik told police he returned to his apartment to find Williams dead.
The papers say Malik, 55, said he choked Williams with an electric cord after she wound it around his neck and struck him with a frying pan.
Prosecutors say forensic evidence will contradict him.
The Associated Press contributed to this report.