My 1997 4runner with the 3.4 v6 had developed a squealing/whistling recently. It will only make the sound above 2500RPM while moving, not while parked. BUT the sound is present with the clutch in or out, in gear and out of gear. I have removed all three belts, alternator power steering and ac, still makes the noise while moving and over 2500 rpm. No exhaust leaks, used a blower attached to the tailpipe and found no leaks anywhere. My simple troubleshooting tells me the issue is something with the engine, not the transmission or clutch or drivetrain related. Possibly an issue with timing belt idler bearing or water pump?

 

Could also be a pulley bearing, but that's the only other idea I've got for you.