I've been wondering if the word "Shinobi" is an accepted English word. As far as I know, its synonym "Ninja" is an accepted English word where "Spy" is the nearest common English.
Depends on the audience. For a general audience, it seems shinobi would not be understood.
Wikipedia has a list of English words of Japanese origin, and shinobi is not on that list, not that educated native speakers would be expected to know all those words, however.
Some native speakers of English who are pretty fluent in Japanese (such as myself) don’t even know the word shinobi. Just don’t read much about ninjas, I guess.
However, in the context of ninjas, shinobi does seems to be understood. Here is a book title at Amazon that uses the term:
The Secret Traditions of the Shinobi: Hattori Hanzo's Shinobi Hiden and Other Ninja Scrolls