Baby Bowser was never Mario's boss, he was the boss of Yoshi's Island and Yoshi's story, so he was Yoshi's boss. You're probably thinking of Bowser Jr. Who was a boss character in Sunshine, NSMB and Galaxy. He's also the coolest Nintendo character ever. Although I've never actually met anyone who agrees with me
King Boo was never a Mario (final) Boss either. He was the boss of Luigi's mansion. Luigi's boss. Even then, it was also Bowser.
To add some missing faces that Mario has fought, how about Wart, Cackletta, Tatanga, Count Bleck, Smithy or Master Hand...
Anyway... My vote is, of course, Bowser. It's always been Bowser.
"What's a finale without a Bowser appearance, huh? A cruddy finale, that's what"
Bowser, Paper Mario: The Thousand Year Door
I love the way he was portrayed in the Paper Mario games, so full of character and funny.