This is a very imperfect solution (and subject to the same issues you noted above) but on 9/12/17, united.com is showing availability on JNB - ZRH - BOS arriving into Boston at 3:20pm.
There are a few other Boston options as well including JNB - GRU - YYZ - BOS on SAA connecting to Air Canada.
It would at least give you something even if it meant paying for the BOS - NYC flight at the end.
Ditto on that same day if you use YYZ as a destination. Options including JNB - MUC - YYZ on SAA to AC.