In 1838 Calvin Tomkins and his brother Daniel purchased approximately 20 acres (81,000 m²) of land, located in a cove north of the Stony Point promontory, underlaid with rock suitable for burning along the river shore for the purpose of making lime. The village grew around the works and when the post office was opened at this site, it was named after the founder’s name and its location.

According to some geologists from that time, Tomkins Cove had the purest limestone formation in the world, except for certain deposits in Russia.

The Hudson River National Defense Fleet established by an act of Congress in 1946, was first located off Tarrytown, one of eight anchorages in the United States to provide a sizable group of merchant ships to support the military effort at the outset of any war. On April 30, 1946, the Hudson River fleet was moved further north to Jones Point (at one time known as Caldwell’s Landing) at the foot of Dunderberg Mountain. The fleet was at its peak with 189 ships in July 1965. Anchored in ten rows, it extended from the fleet office at the Jones Point dock several miles to the south – to the Boulderberg House at Tomkins Cove. Several viewing points were established along Route 9W for the hundreds of motorists who stopped daily to look at the ships. The anchorage remained until the last two ships were towed away on July 8, 1971, to be sold for scrap to Spain.