In some ways, yes.
1. Ninja did not always go running around in those black masks and suits- they were more often disguised as traveling monks, entertainers, etc. (because that made for a better cover and could get you into more places in broad daylight).
2. Ninja were hardly glorious- they were more of a mercenary force.
But in other ways, no.
1. They WERE badass.
2. They DID have amazing special tools that enabled them to sneak, climb, and attack effectively.
3. They did have region-specific clans like in Naruto (am I stretching it? Probably).
Haunty on HubPages has some fun ninja Hubs; I highly recommend them.