I guess the Dark Brotherhood and the Morag Tong are in the same vein, but really there's nothing that's even close to a perfect cognate for ninjas. Sorry. :-(
Men'Do PC NA AD Khajiit
Grand High Illustrious Mid-Tier PvP/PvE Bussmunster
There is none in game, but you are welcome to create your own - a guild of samurai like assassins wielding 2H katanas and Akaviri armors. Only dark horses allowed.
PC EU (PL): 14 characters. ESO player since 06.08.2015. Farkas finest quote: "Some people don't think I'm smart. Those people get my fist. But you, I like."
As other people have said the Dark Brotherhood and the Morag Tong are similar in the sense that they're secretive groups of hired assassins. But they're politically neutral (they may assassinate political targets - but because they were paid to do so, not because they're part of an opposing faction) and they don't do espionage, sabotage or other stuff typically attributed to ninjas.
If you mean something like the typical depictions of ninja in pop culture - guys who wear all black, use a special (often secret) form of martial arts and daggers, may have special abilities like invisibility, exceptional climbing skills etc. then there isn't really anything. The nightblades are similar in some respects, but they're not an organised group.
If you wanted to make a ninja your best bet is to make a nightblade and have them join the Dark Brotherhood.
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