Ninja
A ninja is the Japanese equivalent of a commando: an individual trained to perform under exceptionally adverse circumstances.
Originally the ninja were assassins and infiltrators working for daimyo and shogun alike. Many had some magical knowledge and martial arts training that exceeded military practice. Some were merely highly competent but otherwise 'normal' humans with little exceptional skills beyond raw talent.
The Shinobi is a title as well as a class of rank. Shinobi serve a patron deity of the Shinto pantheon. They are selected from the ranks of the finest pupils, selected for intelligence, initiative, physical or magical prowess, and devotion. The particular skills and abilities of the Shinobi vary widely from one to another.