I've always preferred the term "Skipper", especially when heading out on a "three-hour tour".
However, we might note that the COLREGS and Inland Rules don't mention "Captain" or "Skipper", and use the term "Master" only once (w/o definition). Also, as I recall, a Merchant Mariners License specifically allows one to "Master" a vessel of x-tonnage.
Word Origin & History
1375, "one who stands at the head of others," from O.Fr. capitaine, from L.L. capitaneus "chief," n. use of adj. capitaneus "prominent, chief," from L. caput (gen. capitis) "head" (see head).
So, apparently, the "Captain" is simply the "leader" of the folks on the boat, the person nominally in charge, etc. As in Whitman's "O Captain My Captain".
Of course, that doesn't mean that the person holding the "real power" isn't the "Admiral," or "She-Who-Must-Be-Obeyed."
It's in the lazerette?
Oh, never mind...
I didn't REALLY need it anyway.