Unagi The Eel

Unagi The Eel is an alternative boss of most water-based courses. It functions similarly to the regular enemy version but will instead chase the player. It is usually defeated by being run into using the metal cap 3 times.

Jolly Roger Bay
Works as listed above.

Dire, Dire Docks
Works as listed above. If fought in Jolly Roger Bay, it will have a bandage on it's head.

Drip, Drip Cave
Works as listed above. Will take 5 hits instead of 3.

Unagi Caves
Works as listed above. Generally only appears when all 3 previous fights have been won.

Shady Shallows
Works as listed above. Some reports claim it has a second phase, though what this second phase is, when it triggers, and what happens is unknown.

Trivia

 * One of the few alternative bosses that are regular enemies in the standard Super Mario 64 copy.