While deciding on exactly what weapons the ninja will have on him, I came across the game "Ninja Blade". I've noticed that the character in the game carries the weapons I had originally planned to give my character. I realise that ninjas do carry a lot of their weapons around with them most times, not they simply cant have everything! which is why Im narrowing down.
The weapons I wanted to give my character were
A traditional short ninja sword
A really strong katana, taken from a samurai warrior victim killed sometime before.
A Manriki Gusari
A Vigoorian Flail
(both of these weapons are swung around, a bit like nunchuka, However the flail slices the opponent while the Gusari is used to knock someone out or entangle them)
Here are some videos of some of these weapons in action, for those who are not familiar with these weapons.