1) Wear all black.
It’s so easy to think of a ninja all in black, hood over face, that even books and other resources who get other historical details right usually fall for this one. The truth is, in pre-modern times, black clothing was both rare and expensive. (It takes a lot of dye to get cloth really black, so it costs a lot.) Even if a ninja could afford an all-black outfit, he or she wouldn’t be likely to wear it on a mission.
In feudal times, the Japanese did have access to indigo as a dye, so dark blue would not have been uncommon or rare. For a night mission, that might have worked well. But most of the time, a ninja would probably have been wearing clothes that let him or her fit in–looking like a farmer, a peasant, a beggar, a monk, a nun, or whatever else would be inconspicuous. A successful ninja = someone who doesn’t look like a ninja. That means dressing like everybody else.