Authorities say the 56-year-old Shabazz was found just after 4 p.m. inside of her Midwood home on East 28th Street by her daughter.
The death does not appear suspicious, and Police Commissioner Dermot Shea said she had been ill for some time.
"At this point in time, working with other authorities, the medical examiner, and speaking to the family, she had been ill for a period of time," he told PIX. "And at this point, nothing appears suspicious."
Police are "absolutely not" looking for a suspect, he added.
Family members told first responders that she had possibly experienced food poisoning earlier in the day.
"We are investigating, and the cause of death is pending the final results of additional testing," Julie Bolcer, a spokeswoman for the Office of the Chief Medical Examiner, told ABC News. "But the death does not appear to be suspicious following initial review."
Bernice King, daughter of Martin Luther King Jr., took to Twitter saying, "I'm deeply saddened by the death of Malikah Shabazz."
Shabazz's death comes just days after two men were exonerated in the 1965 assassination of her civil rights icon father, after a nearly two-year-long re-investigation.
Muhammad Aziz, now 83 and previously known as Norman Butler, spent 22 years in prison before he was paroled in 1985.
2 men convicted in Malcolm X's 1965 death exonerated
A co-defendant who also maintained his innocence, Khalil Islam, died in 2009.
"It's so horrible," Mayor Bill de Blasio said. "It is so painful...I'm sorry for what (the family is) going through right now, and any way we can support them, we all need to."
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