The only known ninja on the island is JesusthePirateNinja, there may be other ninja1) in hiding. Rumors persist of an alchemist2) who is the nemesis of all ninja.

1)
The plural of ninja is, oddly enough, ninja. Unless you're talking about the ones from Spain who serve Vega, which are, indeed, ninjas.
2)
He does not appear to have the Philosopher's Stone, or else isn't telling us where he hid it. Perhaps he ate it. I hear they're quite tasty. But few have tried to cut him open and lived.