From "Ninja: AD 1460-1640, by Stephen Turbull. Osprey publishing 2003"
Standard ninja equipment:
-katana: could act as both sword and shield, the length and curve would vary, usually a ninja would choose a blade that was shorter and straighter than usual.
-other weapons or equipment:
-utility belt
-folding fan (which might conceal a knife blade)
-tekagi: heavy iron kunckle-dusters
-hooked rope
-shuriken (stars)
-tetsu bishi (caltrops): iron spikes arranged in the shape of a tetrahedron, good at slowing down pursuers.
-poisons/antidotes
-emergency food supplies
-saoto hikigane: portable listening devices which acted like ear trumpets
-hamagari: long thin saw -- often used to open gaps
-tsubokiri (breaking and entering tool)
-kurorokagi (a metal climbing device)
-shinobi-gama: sickle weapon derived from the sickle and chain
-hokode (hand claws)
-bow/arrow
-specialized geta for special purposes
"Ninjas also had to be fully conversant with firearms and explosives technology."
I don't have any clue when and if the ninja villages of Iga and Koga were removed. They were for a time mercenaries for hire before falling under the Tokugawa shogunate. The last battle they are noted to have fought along with samurai was in Shimabara in 1638.
