Hi folks, I'm from Japan and hopefully I can shed some light on this. The word 'ninja' comes from Chinese characters 'nin' meaning blade, and 'sha' meaning person. Translated into English, it simply means assassin. Ninjutsu's jutsu means method, or basically the method of assassination. So basically a ninja is an assassin trained in assassination...nothing more. In older Japan, before the Meiji restoration period, Ninjutsu was predominantly taught in 2 areas, the Koga prefecture (now Mie) and Iga (now Shiga).
The concepts of stealth and quick killing are vital to assassins. Ninjas used knifes, blades and other weapons simply because guns were not available at that time. The normal concepts of good health and skills are obvious. Most of the ninja stories are exaggerated though. The shuriken or throwing star is a fancy hollywood adaptation of asian mysticism. The shuriken is a perfect weapon for home defence if you are attacked by a blind quadriplegic.
Ninjutsu is not a martial art like Karate or Jiujutsu; it is more of a profession. A modern day ninja is not a person who dresses in black, does fancy sommersaults, uses smoke bombs and stuff. Watch the movie of Jean Reno called 'The Professional', this will give you an idea of what the Ninja is. The idea is simple, maintain no relations with anybody, accept contracts, kill without being killed, watch your ass at all times...etc etc. A long range gun with a silencer and a good aim is probably the best weapon for a ninja.
I have not heard of any reliable ninjutsu schools, but there are quite a few arts that claim to teach the art of survival...eg. Krav Maga. You never know though, there might be something to this; just because you dont know something, does not mean it doesn't exist.