Shoe goo did good with straight rubber boot repairs for me. Not sure how it would adhere to the joint between the nylon and rubber.
To double up on the repair, you might want to use a small amount of the aquaseal or shoe goo, let it cure, and then add a piece of good gorilla tape over it.
It works well on my pool cover when I want to stretch it out for another winter before pitching it. As long as I cleaned the cover real well and wiped it down with alcohol, the gorilla tape adhered nicely and waterproofed the pool cover pin holes.
http://www.amazon.com/Sho...-7-Black/dp/B004PBOJE8