@HDMI1 he's properly documented as a Samurai and ninja are known to exist way before him, though. The Mysterious generals of Yukimura are the ones who are suspected of trully being a Ninja. There's nothing on them prior to their presence at Yukimura's command and all of them were adapted as ninja in modern stories as well. Sarutobi Sasuke, Kirigakure Saizou, Kakei Juzo, they are all a part of Sanada's Ten Braves a novel written during the edo period, and their names are similar to those of warriors that were in fact under Yukimura's command. Of which little info is actually known about.
Then there's an actual ninja in Kotaro Fuuma, the only one who was an actually known ninja, and had his own group operating during the Sengoku period. This guy operated under the Hojo clan, I believe.