Police say Shabazz, 56, was found inside of her Midwood home on East 28th Street by her daughter just before 5 p.m. ET.
The death does not appear suspicious.
Bernice King, daughter of Martin Luther King Jr., took to Twitter saying "I'm deeply saddened by the death of Malikah Shabazz. My heart goes out to her family, the descendants of Dr. Betty Shabazz and Malcolm X."
I’m deeply saddened by the death of #MalikahShabazz. My heart goes out to her family, the descendants of Dr. Betty Shabazz and Malcolm X.— Be A King (@BerniceKing) November 23, 2021
Dr. Shabazz was pregnant with Malikah and her twin sister, Malaak, when Brother Malcolm was assassinated.
Be at peace, Malikah. pic.twitter.com/YOlYoW4xDC
Shabazz's death comes just days after two men were exonerated in the 1965 assassination of civil rights icon Malcolm X.
Muhammad Aziz, now 83 and previously known as Norman Butler, spent 22 years in prison before he was paroled in 1985.
A co-defendant who also maintained his innocence, Khalil Islam, died in 2009.
Malcom X was killed 57 years ago in the New York City neighborhood of Washington Heights.
Shabazz was one of Malcolm X's six daughters.
ABC News contributed to this report.