Ninja is a phrase now used to label a person you do dirt with. It's roots are found from the actual Ninjas who would move in the darkness of the night, never being seen, veiled in mystery, also usually committing crimes as Ninjas were actually farmers who rebelled against the Samurais who were rich men, soldiers, and basically part of the Govt. Now the phrase is used more commonly to friends who you may be committing crimes with and crimes usually happen at night. If you commit a burglary then those affiliated with you could be called your ninjas. Of course, a lot of people just want to sound cool and use the phrase though never committed any crimes in their actual life. So the phrase has also become just another word similar to words and phrases like homey, homeboy and nigga.
I just called up my ninjas, we bout to rob them fools.