^ 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.