The term ninja (kanji: 忍者) means "stalking/hiding person" in English. It is written にんじゃ in hiragana. It's pronounced roughly like "neen-jah".
Literally, one who stalks or hides. 忍 is more commonly used as the verb shinobu, 忍ぶ. Besides the meaning of “to stalk/prowl/hide,” it also means “to endure/suffer,” especially without showing one’s emotions.
者, by itself, is mono in the Japanese reading and means person. The Chinese reading is sha; it becomes ja in this case due to the linguistic phenomenon of sequential voicing.