I've read about Hatsumi and Hayes, but I'm sure that neither of them are taken seriously within Japan's historical community. So, have there been any books or papers from trusted academic sources on the ninja and who they were recruited from, weaponry, etc. I'm not looking for a book or paper in a single language. I'll use a Japanese source.
I haven't read them yet, but I've heard real good things about Antony Cummins' books. He's a historian on ninjutsu.
hi! you'll find a few source references sprinkled through /u/asiaexpert's comments in this AMA-like post:
The respective roles of Ninja and Shinobi
and a couple more here
Was there any significant role of ninja on the actual battlefield?