This is supposedly not uncommon on the V6 trannys. I don't know if its the bearing or the fork that makes the noise. Mine used to do it too but hasn't done it since I replaced the clutch w/ new bearings and I greased the fork fingers. I've heard of people removing the fork boot and spraying lube in there to make it go away, but I don't know if that's a great idea. Lube getting on the clutch itself wouldn't be good.

'97 4Runner, '06 F350, '86 4Runner, '05 WR450
http://home.4x4wire.com/erik