Quick Question, were ninja still active during WW2? If not, when did they stop being utilized? If so, any accounts worth sharing?
There is no evidence to support the ninja being active much further than the Edo Period. Fujita Seiko was claimed to have taught ninjutsu at Rikugun Nakano Gakko (Nakano School for Military Intelligence), but there's no evidence to support these claims.
Essentially, the historical record of the shinobi ends with the Shimabara Rebellion (1637-1638). "Men from Kōga" were employed by Tokugawa Iemitsu to steal into and survey Hara Castle.
There are similarities between the ninja and the Oniwabanshu (Garden Keepers – the secret intelligence service of Tokugawa Yoshimune in the early 18th century); however, there is no evidence from contemporary records naming the Oniwabanshu as shinobi.
Edit: A Last Account of Shinobi
Unfortunately, I can't effectively corroborate this story. It was told to me by a friend after he visited the Iga Ninja Museum in Iga-Ueno, while explaining a picture of a document in, if I recall correctly, Portuguese.
Toward the end of the Momoyama Period, Japan began to close itself off. Before the Portuguese were effectively kicked out of Japan following the Shimabara Rebellion, a small cadre of shinobi were sent onto a ship to steal what was believed to be important documents proving espionage. Supposedly, since none of the agents could read Portuguese, what they came back with was a hand written document in Portuguese that amounted to a bawdy poem.
Supposedly, this was considered a complete disgrace, and signaled the beginning of the end for the shinobi as reliable agents.
A ninja is simply an assassin. They still exist today in some sense. I don't have any facts, but I wouldn't be surprised if the Yakuza has people silenced by assassins. Maybe just with guns instead of ice blasts or fire from their mouths.