Well, the minibosses typically provide the item of the dungeon--which in Ganon's Tower, the maze with Phantom Ganon had provided the Light Arrows, so I'd consider that the miniboss. And besides, bosses usually have some sort of cutscene and Puppen Ganon definitely had cutscenes. Kind of like some of the other Zelda games, the Wind Waker had a multi-battle final boss. Not too different from Ocarina of Time, Twilight Princess, and many others. Nintendo seems to like that formula for final bosses. So, I'd say Puppet Ganon is a boss.