A ninja is, in Japanese history, someone who uses untraditional arts of war. They were spies and assassins.
While the pop culture description sounds like the average PPC Agent (particularly those in the Department of Mary Sues), there's really a large difference between the average ninja and the average Agent, including levels of competence and insanity.
Some Agents are ninja, due to their home continuum, but they usually do not reflect the pop culture idea of a ninja.
Miss Angel, of OFUTRC, is a ninja, as are several of the Canons.