The link didn't seem to work for me. But, I'm wondering why it would be
the driveshaft itself instead of the universals?

The drive shaft has a slip yoke that is supposed to slide smoothly fore and
aft. If it binds, you can get a latent clunk when it eventually frees up,
usually after a hard stop. I had the issue with my F250 and it was solved
with lubrication. I also had the issue with my Lexus GX 470, and it was
solved by replacing the driveshaft with a newer designed unit. Like John
said, it's a very common problem on the 4Runners and GX 470 (same
drivetrain). Lexus has a TSB on it and when I took mine in for its 5000
mile service, the dealer performed the TSB at my request, with no charge and
no hassle. By 5000 miles, mine was just starting to show signs of the
clunk. No problem since the driveshaft was replaced.