If you're dead-set on getting rid of it then I 2nd parting it out. There's no other way to gain more money than parting out a vehicle if there's any major problems with it (ie. blown motor, major body damage, etc).
The drivetrain and interior alone would get you more than $1000 IMO. Chances are you could still sell it to the scrap yard for the same price after that. They're only concerned with how much scrap steel they'll get out of it.

If you don't want the hassle of spending the time parting it out perhaps you may have a friend that would do it for a small fee or percentage.

Like others have said as well- this could be a perfect opportunity to do an engine swap if you like your Runner. You may be sick of it, but with a 3.4 it would be like having a completely different vehicle.

Either way, I hate to see the 2nd gens going to waste when there's a lot of parts people are searching for that are no longer made.

And to end my soapbox rant, I hate hearing of people having to drop up to 2 grand just to have the heads redone. You could put a reman engine in there for the same price.
Just a thought

Whatever you choose, good luck!

~R