The word ninja comes from the two Kanji characters.
These two words, when read in japanese pronunciation, read as Shinobi-no-mono while when read as chinese pronunciation they read nin-sha.
While, the word mono and sha mean person.
So if you read the Kanji characters as native Japanese or Chinese derived pronunciation mean the same, that is someone who is stealthy, someone who is silent (not just in literal sense, but like quiet as sea) or a person who endures.
In modern Japanese, they are usually referred to as Shinobi.