"Ninja" were mainly samurai doing spy shit. They might disguise themselves as peasants, but usually they were from the warrior caste acting on behalf of their lord. The whole "sneaky guys in black pajamas" was something that came from plays where people playing ninjas would dress in black to hide in the background of a scene. Then they would enter the stage and it would look like they appeared out of nowhere.

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.

Not to my knowledge, but as I said I have mostly failed at successfully researching them. I think ninjas were mostly peasants and samurai working on behalf of warlords, whereas the Ikko-Ikki was more of a grassroots movement.