I think ninja's were originally just a bunch of Japanese farmers that were sick of being bullied by passing samurai. Their weapons are modified farming tools. Iga and Koga are the 2 famous ninja clans.

I grew up watching ninja movies, so when I found out there was a ninja museum in Iga (Iga Ueno in Mie Prefecture), I couldn't get there fast enough. There's not much to see in Iga besides the ninja museum and a feudal castle, but it's a nice place to escape to if you've been stuck in one of Japan's larger cities for awhile.