I run into the same problem all the time 'cause I like to use junk-yard MII and Pinto x-members and suspensions in my cars. And I have yet to find a source for new boots! I agree it is unbelievable that no one sells them separately but I have never found a source and trust me, I have looked. I guess they assume that if the rubber is that bad, you should replace the joint which is assumed to be bad too.
My solution is to scavenge a handful of good used boots from Pick-A-Part every once in a while to keep in stock.