The main character in "The Isle of Pingo Pongo" is a goofy dog named "Pingo" who lives on an island with his friend "Jesse". Jesse is usually portrayed as a well-meaning but clumsy human.
While not a boat, their home is a ramshackle hut on the island, and the episodes often involve Pingo and Jesse getting into wacky situations.
Let me know if this is the show you were thinking of!