I have a pair of Cabelas waders that have a small leak at the interface of the cloth and the boot top.  Aside from buying a new pair, what's the best way to stop the leak?

I'd suggest barge cement or Shoe Goo

Shoe Goo (aka Household Goop) is my go-to adhesive. This stuff has extended the life of my shoes many times; the bottoms wear out faster than the uppers, and a coating of Goop saves them! This stuff will mend a broken heart!

OP, it's like very thick airplane cement (thicker than honey). It can be easily applied with an acid brush; it sticks anywhere you put it. I have repaired rubber balls with it simply by applying it like a patch over the rip.

Clean the surfaces first.

eta Sold in Home Depot and other fine stores across our Nation!

Wally world sells shoe goo.  If it will handle the abuse I have put it through on my tennis shoes, it will stick to a wader and seal it.  

It is still holding the sole on my pre-china, USA made Chuck Taylor shoe. 

Neoprene waders shoe goo, Goretex waders a bicycle inner tube patch, glue it light it and call it good.