John was born to Drake and Abigail (Howe) Miller. Drake was the son of Lemuel Miller, who was the son of Stephen Miller, who was the son of Johann Mueller who came to this country from Holland and settled on the Tappan Zee, near Tarrytown, on the Hudson river. In 1824, John married Phoebe Tillotson, whose ancestry can be traced back to the Lords of Tilston Manor in Cheshire, England. Phoebe died in 1851 giving birth to their 12th child. A few years later John married Maria (Purdy) Bogardus, widow of William Henry Bogardus.

In his later years, John with his wife, Maria, traveled west to visit his children that were living in Minnesota. They stayed with John's son Hiram in the small town of Douglas just outside of Rochester, Minnesota for a little over a year. In the summer of 1871, John's health began to decline. He passed away in October of 1871 and his wife afterwards returned back to New York.