While the cause of death has yet to be officially announced, US media are reporting she was found hanged.
Mary Kennedy had four children with Kennedy, the son of the late Senator Robert F Kennedy and nephew of President John F Kennedy. He is a prominent New York environmentalist.
A statement issued by Mary Kennedy's family said: "We deeply regret the death of our beloved sister Mary, whose radiant and creative spirit will be sorely missed by those who loved her."
And in a statement released by Robert Kennedy Jr's chief of staff, the family said Mary Kennedy, an architect, "inspired our family with her kindness, her love, her gentle soul and generous spirit."
"Mary was a genius at friendship, a tremendously gifted architect and a pioneer and relentless advocate of green design who enhanced her cutting edge, energy efficient creations with exquisite taste and style," the family said.
Officials said Ms Kennedy, who had fought drug and alcohol problems, was discovered by police in a building at the Kennedy property in Mount Kisco.
A lawyer for Mary Kennedy said she and Robert F Kennedy filed for divorce in 2010 but that it was never finalised.