Or am I wrong, and in fact the prophecy comes from a more recent time, after the boy was taken to Blackwing and made friends with Dirk?
While this is a plausible explanation for the prophecy featuring Dirk, it doesn’t explain how the prophecy can predict:
[…] once the great dark wizard found his apprentice, no one in Wendimoor could defeat him, and his army would come like a tide.
The only hope to save Wendimoor is if the fiercest of foes were united, the great weapon is retrieved, and she who sees all opened a door into a dream, allowing through a man, who, with him, would bring a boy, […]
All of this only happens after the prophecy was first mentioned (in the very first scene of Season 2).
While some of this can be attributed to educated guessing, prophetical vagueness mixed with confirmation bias, and self-fulfilling prophecy, it is unlikely that the Boy would get it all right by means of deduction or orchestrating the events.
The only thing that the Boy’s connection to Dirk Gently can explain is why the prophecy is so specific regarding his name, but not with respect to everything else.
However, the fact that Dirk Gently is constantly referred to as Svlad Cjelli by Project Blackwing suggests that he only took on this name after leaving Blackwing.
Thus, the Boy should not have known Dirk Gently under his current name.
Now, on the other hand, the Boy is able to create persons and things with real supernatural powers or properties:
The Mage is actually a mage, even when he comes to our world.
The airgun can actually be used as a weapon.
The pocket dimension at the Cardenas’ house and the flying purple people eater are what they are.
Most importantly, Wakti Wapnasi has actual magic powers (somebody says that she and the Mage are the only such persons in Wendimoor).
During the events of Season 2, she uses them to connect to our world.
With all of this, it seems plausible that Wakti Wapnasi – who made the prophecy – also has actual prophetic powers.
So the answer to your question is:
It is an actual supernatural prophecy.