[sirdarksol]

Depends on what you mean by "real."
The "rank" of ninja lost its point about the same time that the samurai lost their swords and titles. Because of this, the traditional clans of ninja faded away. They were, ultimately, financial entities, and when the money went away, so did the clans.
However, as with many other arts that lost their practical purpose, there were those who were dedicated to the art, rather than the position or the money or the power. These people could very well have continued the practice of the art, even as it became pointless from a pragmatist's point of view. Due to the fact that these people were, by nature, secretive, it is also quite likely that this practice would go unnoticed.
Add to this the Meiji debacle...I mean, Restoration, which was a historical purge of the unsavory elements that built Japan in an attempt to make it look like Japan's creation was free of the blood and horror that was involved in the birth of every other nation on the planet, and records of such people could very easily have disappeared, whereas the more "noble" arts, such as kyudo and kenjutsu were seen as acceptable elements of the past.