From
WikipediaThe coxswain is the person in charge of a boat, particularly its navigation and steering. The etymology of the word gives us a literal meaning of "boat servant" since it comes from cox, a coxboat or other small vessel kept aboard a ship, and swain, which can be rendered as boy, in authority.
Skipper
A skipper is a person who has command of a boat or sea-craft or tug, more or less equivalent to "captain in charge aboard ship." At sea, or upon lakes and rivers, the skipper as shipmaster or captain has the absolute command over the crew. The skipper may or may not be the owner of the boat.
The word is derived from the low German and Dutch word schipper; schip is Dutch for "ship". In Dutch sch- is pronounced [sx] and English-speakers rendered this as [sk].
The word "skipper" is used more than "captain" for some types of craft, for example fishing boats.
It is also more frequently used than captain with privately owned noncommercial or semi-commercial vessels, such as small yachts and other recreational boats, mostly in cases where the person in command of the boat may not be a licensed or professional captain, suggesting the term is less formal. In the U.S., a "skipper" who is in command of a charter vessel that carries paying passengers must be licensed by a state or the USCG. If the vessel carries over six paying passengers, it must be an "inspected vessel" and a higher class license must be obtained by the skipper/master depending on the vessel's gross tons.
In Navy/Marine Corps and merchant naval slang, it is a term used in reference to the commanding officer of any ship, base, or command regardless of rank. It is generally only applied to someone who has earned the speaker's respect, and only used with the permission of the commander in question.
Skipper RNR was an actual rank used in the British Royal Naval Reserve for skippers of fishing boats who were members of the service. It was equivalent to Warrant Officer. Skippers could also be promoted to Chief Skipper RNR (equivalent to Commissioned Warrant Officer) and Skipper Lieutenant RNR.