Prove me wrong, s14 sr20 tranny noise
 

Tell me if you think Im wrong or right on this one;

Rear output shaft seal was leaking, drove couple hundred kms on it, noticed whining noise from tranny only when in neutral.
As soon as you engage the clutch(depress the pedal) the noise will go away. You can hear it in gear while driving, not super loud, but definatley at idle, clutch out, the noise is there , clutch in noise goes away. Doesnt matter in or out of gear while clutch engaged not driving.

Input shaft bearing on the tranny?

Shouldnt be release bearing or pilot bearing but if you think it is, please tell me why.

Could also be a noisy throw-out bearing...

100% the throwout bearing. Mine is shot too, I just dont have the time or resources to swap it right now.