I believe that it's just a straight nautical tie between Skipper's -- the chief of boats -- and the fact the manager is chief of the team.
The Team itself can be considered his boat.... I don't know if there was a specific incident that led to the popularizeing of Skipepr being used to term a manager, but the comparison between Captains of boats and Managers of teams shoudl be pretty clear.
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Red Sox
Sixty-six representatives of the Giants (55 players and 11 managers) have been inducted into the Baseball Hall of Fame, more than any other team in the history of baseball. The Dodgers franchise is second (45 players, 9 managers) and the New York Yankees are third (41 players, 11 managers).
America's Team
I have never heard of a manager which didn't play baseball, and I can't imagine a team hiring someone who didn't play, but im not sure that no one who manages hasn't played.
As of June 2014, the Boston Red Sox has had 12 different owners since the team began in 1901. The team has had 46 managers.