This is a halyard chantey. The type of rhythm and the lyrical content indicate that slaves in the West Indies or in the Gulf states originally sang this song. In fact, when John Cherokee is referred to as an "Indian man" it probably means he was from the West Indies. Sailors might have learned the song from freed slaves who joined the ship's crew or from black waterfront workers in the Southern states. It depicts the brutal treatment that many men faced at the hands of the captains and mates.
It is included in the Roud Folk Song Index as #4693.
Stan Hugill sang "John Cherokee" on his album Stan Hugill Reminisces. It was also recorded by The Hardtackers from whom I learned it.