The cultural phenomenon that we recognise as the Ninja, is almost totally a fib; perpetuated by the same cultural forces which set it in the public conscience in the first place.
Historically there are very few instances of accounts of ninjas. Mostly they were recruited from the peasantry in Japanese society and were not particularly notable at all.
There appears to be a blurring somewhat between what we understand samurai to be and that of the ninja. Samurai lived by the code of "bushido" which means the "Way of the Warrior" and was marked by a very distinct degree of chivalry, nobility and honour until death. Whereas ninjas never followed such a code and the art of "shinobi" was one of covert operations and secrecy. The word shinobi means "to steal away" and reflects the "invisibleness" of the ninja.
The truth is that most ninjas would have worn hard wearing navy blue overcloaks and hoods and the reason why we portray them as wearing black in the West, comes from the tradition in Kabuki and Noh Theatre that people wearing black are invisible.
For the most part Ninjas themselves usually didn't go around killing people, that was the job of hired samurai. Ninjas were more likely to dress like farmers, priests or shopkeepers and usually went around in disguise in plain sight.
A ninja disguised as a farmer would be more likely to carry an axe or a sickle than to wield a katana (swords used by samurai).
Ninjas were probably more likely trained in the art of distraction, such as clanging pots to divert attention, so that a samurai could kill someone, than they were to actually do any killing themselves.
More Likely to be a Ninja
The truth is that our perceptions have probably been shaped more by theatre and television shows like Phantom Agents and The Samurai Shintaro* than historical fact.
*Shintaro did claim to be a Samurai though