so basically, we're looking at where the character's themselves, from their story come from and not the company that developed the game in which the character comes from?
Alright then.
Trying to think of some ninjas now...
Besides the original example of america's ninja(MGS) which by the way, there's no guarantee that the cyborg ninja was developed in america, considering most MGS games happen no where near america...except MGS1... I always forget is alaska is part of the USA or not... (And I am talking story within the game)
Anyway, besides that example I'm having serious trouble thinking of ninjas that DON'T come from Japan...