I have a tranny leak on a 700R-4 at the rear where it meets the drive shaft. Is there a rear transmission seal there that can be replaced? If so, is it difficult?

There is a seal there, replacing it is pretty easy.

Is it a seal that attaches to the drive shaft or is it inside the trans tail shaft? Any special tools required?

It's inside the tailshaft housing. Something to pry it out and something to drive the new one in without damaging it are all you need.

Would I be able to pick up the seal at any parts store, like Pep Boys or Auto Zone? I couldn't find it on the Auto Zone web site.

I'd expect they'd at least be able to order you one.