No, ikko-ikki were the local self-defence groups made of petty samurai, armed monks and peasantry in the Sengoku era, they were reaction to feudal warlords doing usual warlordy things.

Ninjas, more properly called shinobi, were just medieval kind of intelligence operatives working on behalf of usual feudal lords. They mainly did spying and occasional assassination or sabotage, and didn't dressed funny.