Ailina Tsarnaeva, of North Bergen, New Jersey, made the threat against a New York City woman on the phone, police said.
She later turned herself in and police charged her with aggravated harassment.
News reports said Ms Tsarnaeva told the Harlem woman she had "people who can go over there and put a bomb on you". She will appear in court on September 30.
Her lawyer George Gormley said he would comment later.
Ms Tsarnaeva has been required to report to Massachusetts probation officers since prosecutors said she failed to co-operate with a 2010 counterfeiting investigation.
Dzhokhar Tsarnaev is charged with building and planting the two pressure cooker bombs that exploded near the marathon's finish line, killing three people.