Agree with Mike, in neutral with the clutch out the transmission is spinning. So, transmission shafts are moving and a bad bearing could make some noise. How often has the transmission oil been changed? It could just be low, so change the transmission fluid now and see if it helps.
You might be on the lookout for a used transmission, or start pricing a trans rebuild of the current one. If the noise persists and gets louder at some point you are looking at some transmission work.