OK,
There seems to be a lot of flat out hatred for the ninja. But, as far as I can tell, a lot of it is because it's called Ninja. People who hate anything that remotely whiffs of Anime or Japanese Mythos.
So,
instead of seeing it as an anime class, what else can you do with it without 'lowering' yourself to playing one of those despised Japanophile things. [/sarcasm]
Now then, I'll start us off with an obvious and in-obvious one.
Assassin : Not the sneaky ninja assassin. I mean the cold, calm, collected assassin. Like the one played by Sly Stallone in the movie Assassins. Someone who's stealthy, heavily controlled and paranoid. The guy who blends in to any crowd, slips in and takes you out while you're arguing with a town guard, and is gone before you or the guard realizes you are dead. He's not running around jumping from roof top to roof top wearing pajamas, he's carrying concealed weapons, disguises, and generally doing things you don't expect.
Bodyguard : Not the Secret Service, standing out in front of everyone with obvious weapons (that's actually more the Samurai). Instead, it's the Christopher Chance type bodyguard from the TV show Human Target. He's an expert at combat, highly perceptive, smart, and paranoid. He protects you by being inconspicuous nearby and taking out any threats before they realize he's with you.
Your turn.
Spy/Secret Agent/Secret Police: This is closer to what historical ninja were actually like.