In a direct fight the witness wins. But the nine see time differently and can plan ahead and nudge events in a way even the vex can't. The nine can also pull things forward to the present and affect the past and watch how the future changes. The nine are essentially playing chess at grandmaster level while the witness was playing at master level. The nine are by far more dangerous than the witness.

Your first mistake was bringing up "power levels" in the first place. I intend to make a post going into what I'm about to say for a while, and in much deeper detail, but I'll give you a brief version. The Nine's awareness arose from life in Sol causing vibrations in loops of dark matter that flowed through the major celestial bodies. While they are fourth-dimensional beings, their ability to interact with our dimension and regular matter has hard limits, to the point they will die if they were to enter our dimension from their own. Nevertheless, their power over time and ability to observe it are unmatched. The Witness, on the other hand, was very much a physical being and an immensely powerful creation of Darkness, the result of an entire civilization coalescing their minds into a single gestalt entity, since the Darkness is a paracausal force tied to thought and consciousness. You need to understand that the Nine and the Witness interact with the world [i][b]in fundamentally different ways[/b].[/i] The Nine are not paracausal (though one line in the campaign might have major implications for their relationship to paracausality), but their power over time is something both the Light and the Darkness cannot match on their own.