@Kamelpov and
@givemersspls, Manga and/or anime as well as light novels, or generally anything out of Japan, China, and Korea is going to bolster their culture over anything else. To be honest, this happens everywhere, even in the U.S. We think our things are better than everywhere else. Thus, it should come as no surprise that a Japanese author makes a ninja either the best of the best (Naruto, etc.) or second, third, or fourth best. It's just like making Samurai better than all other fighters, warriors, etc. of ancient times when they're not.
Ultimately, if we're talking about history then I agree with givemersspls, the shinobi were
only really effective during a time when they played against the code of the Samurai. They did things Samurai frowned upon and thus were utilized in wars for assassinations, espionage, etc. This didn't make them the best of the best, just a necessary group of people with a needed set of skills at the time. I would caution you, Kamelpov to not take legend and popculture about shinobi as something that could be attributed to history. Like, givemersspls says, the Navajo Code Talkers baffled the Axis during WWII. This doesn't mean there were no Japanese spies in WWII and prior:
https://en.wikipedia.org/wiki/List_of_Japanese_spies,_1930–45. By the time WWII came around espionage had evolved beyond what it was in the Bushido period. Citing anything from that time is out of touch with what was going on in the early 20th century. To diminish the Japanese ability to spy and collect intelligence during WWII diminishes spies like Takeo Yoshikawa who was one of the spies of Pearl Harbor:
https://warfarehistorynetwork.com/daily/wwii/the-spies-of-pearl-harbor/,
https://www.historynet.com/the-spy-who-doomed-pearl-harbor.htm.
I would argue Naruto gives a reason why ninjas are strong with chakra, etc. With the Samurai being mostly in the Land of Iron, however in that story the Samurai basically are warped ninjas since they got their abilities from the same source as the ninja from what I remember. Ultimately, it's just fiction. Not necessarily pulled from history since historically ninja are considered warped Samurai. So Naruto arguably flip-flopped it. Of course, not being Japanese, I'm going off history books, etc. that I read here.
Examples of Shinobi-like behavior in modernity is pretty much any guerrilla warrior who wages guerrilla warfare or anyone who wages unconventional warfare. Sometimes it works, sometimes they get the life bombed out of them by conventional armies. Sometimes, like Shinobi, they are attached to conventional militaries and governments as spies, etc.
Edited to add: I typed this up while you two were continuing your back and forth and you had already brought up the initial point I was making that "Ninjas are best" is mostly written for the Japanese readers.