^ Skipper's just a nickname. It's not proper to use it in normal military procedure, at least not by anyone other than a CO's most senior officers.
Gebirg is right - the commanding officer of a ship is always called Captain, even if they're of lower rank like Commander (for example, Scott Glenn in
The Hunt For Red October. His character had the rank of Commander, yet everyone on his sub called him captain, because that was his function).
Fun fact: When training for that role, Scott Glenn took a cruise on a real submarine and (prompted by the sub's real CO) gave orders to its crew.