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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 vessels, such as small yachts and other recreational boats, mostly in cases where the person in command of the boat is likely not a licensed or professional captain, suggesting the term is less formal.
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.