Was this an old or young, a gear head or not? In other words, someone you think should know what gear whine sounds like? At least verses other sounds like bearings and such.
A stick shift Tacoma isn't going to be Cadillac quiet afterall. It's my experience that the diffs don't make as much whine as the R150 does or the t-case, at least that you can hear in the cab. Whine by itself isn't a problem. It's just the sound of gear teeth meshing. So it's unusual whine you need to be concerned with.
If the diff is making noise and you found low fluid a worn pinion bearing or perhaps the side bearings would be my concern. The front diff on 1995+ Tacoma is prone to wearing the little needle bearings that carry the inner CV shaft, especially on the driver side since the axle comes out and immediately drops towards the hub. It's not a whine but more of a hum and a vibration you can feel.
Technically all IFS clamshell diffs can have this but it never was a problem with my 1991 while my 2008 got it at pretty low miles. It could also be that in 1995 Toyota flipped the front diff to the left side so now LHD truck drivers are just more likely to hear it.
Or the rear driveshaft carrier bearing, that transmits right into the back wall of the cab. I'd also check levels in the rest of the drivetrain.