I have a 01 forester 5sp with a bad transmission. Will a different transmission from any 01 forester 5 sp work as a replacement or do I have to get the rear diff as well?

What's "bad" about it? Most can be fixed and will last longer than a used replacement....

 

GD

From what I understand, it's a bad bearing in the transfer case.

That's a $35 part and you don't even have to remove the transmission to replace it. You need a better mechanic not a new transmission. 

 

GD

Unless it blew chunks the transfer bearings are easily replaceable.