It's hard to say, as it seems like we have discussed the obvious stuff.
It seems like you mentioned that it happens in both your speakers and your head phones... and that is why I have been thinking it is on the input side.
Now, did you just mention mics are problematic as well? That adds a new twist...
I am beginning to suspect that you are observing various noises that occur for various reasons and that each issue has it's own solution. This makes it more difficult to trouble shoot as it takes a bit of experience to isolate each cause/effect.
Let's start with some basics.
What is you computer plugged in to?
What is your display monitor plugged in to?
What is the MOTU plugged in to?
What are the speaker monitors plugged in to? Are both speakers plugged in to the same power outlet?
Also, if you physically move the speakers does the problem stay with the monitor? (this is a variation of swapping the cables, but also considers whether the noise is being introduced inside the speaker)
Are you sure that the noise issue you hear on the head phone is the noise in the speakers or is it possibly two different noise issues?
You may want to post sound samples of the noise. Some one may recognize it's source by ear.
best regards,
mike