Following Mr. Van Cortlandt’s death in 1700, the land was purchased from his family by Timothy Carll in 1706. The estate was then acquired by Jonathan Thompson of Setuaket in 1758 for the sum of 1200 pounds British sterling for the approximately 700 acres. Mr. Thompson purchased the land not for himself but for his younger son, Isaac. Isaac married Mary Gardiner from East Hampton in 1772. Jonathan deeded half of the land to Isaac upon the birth of his first son in 1773 and the remainder of the property to Isaac upon Jonathan’s death. At that time that Isaac and Mary Gardiner married they more than doubled the size of the original Van Cortlandt house by adding nine new rooms. Judge Isaac Thompson was a prominent member of Islip Town government before and after the American Revolution and later a member of the New York State Assembly. In 1790 George Washington spent the night of April 21st at Sagtikos Manor. President Washington recorded this in the diary he kept of his tour of Long Island.
After Judge Thompson’s death, the Manor was used for the most part as a summer home for the family. His sons and grandsons built their homes in New York City or other places on Long Island. In 1894 Isaac Thompson’s great grandson, Frederick Diodoti Thompson, bought out all the other heirs and became the sole owner of the 1,200 acre estate. He wanted a home where he could entertain on a grand scale so in 1902 he added east and west wings to the house, enlarging it to forty-two rooms.
The last family member to live in the Manor was Robert David Lion Gardiner. He owned the property from 1935 to 1985 when he deeded it to the Robert David Lion Gardiner Foundation. In 2002 Suffolk County purchased the remaining 10 acre property from the Foundation to keep it from being sold to a developer. The Sagtikos Manor Historical Society has a contract with the county to provide general management of the estate including tours, educational programs and research.