1902 USGS map, Saranac quadrant
Showing Negro Hill and Brook and the homesteads of the Black farmers on Swinyer and Muzzy Roads, in italics, the apparent  origin of the offensive place names.
Based on work by Curt Stager based on records in the Vermontville town hall.

John Thomas Brook, formerly Negro Brook, is a small stream that starts midway between Onchiota and New York Route 3 near Merrillsville, flowing west before curving south and joining Ricketson's Brook a mile and a half west of Bloomingdale and eight miles from its starting point.  In the 1800s it was used for transporting logs to the Saranac River via Ricketsons and Sumner Brook.

The brook has been renamed for John Thomas, a Black farmer who settled the area in the 1860s, aided by Gerrit Smith.

Before 1963, it was known by the more offensive form of its recent name.  The 2023 name change to John Thomas Brook was the result of a request by Paul Smiths College professor Dr. Curt Stager.  It has since been proposed to rename Negro Hill to "Murry Hill" after Wesley Murry.