The history of St. John's Church - and of Cold Spring Harbor itself, for that matter - is dominated by the Jones family. The very first Vestry minutes, written in fine script on September 4, 1831, list the founders who pledged $2,000 “for the purpose of building an Episcopal Church within the vicinity of Cold Spring on Long Island .” Of the first fifteen names, twelve carried the Jones surname, and two others are a married sister and a brother-in-law who married another Jones. Two, Joshua J. Jones and Charles H. Jones, gave no money, but instead gave “the amount of land for the church Burying Ground belonging to the estate of the late John Jones, deceased.”

If one had stood on the hill of that three-fourths of an acre “at the end of the lower mill dam on the edge of St. John's Lake overlooking the salt meadows and the harbor,” it is likely that virtually all the land that a person could see in all directions was owned by the Joneses. That certainly included all that is now Cold Spring Harbor Laboratory, the Fish Hatchery, the steep hill to the west of the church, St. John's Pond to the east and on it the 1698 farmhouse that would one day become the Rectory. The mill, the hardware store on Bungtown Road and, yes, the first whaling vessel to sail from the harbor – all were Jones property along with far more land than the eye could see.

The Jones family influence extended into Manhattan, where the family members were prominent as businessmen, judges, military officers and leaders in Trinity Church at the foot of Manhattan – the church that would become covered with ashes and emerge as the spiritual rallying point following the attack on the World Trade Center in the then distant 21 st century.