I just had my truck on the road, and it has a whine in first and second (a little different in drive or coast in each gear,) but it disappears once I get in top gear. I recall it being pretty typical for these old 3-speeds, and I'm not going to worry too much about it.
If your noise happens in all gears if may be either an input or main output bearing, and in neutral that takes the output bearing (and possibly the differential if you're moving) out of the picture. Repairing the input bearing is a pretty easy task.
