I think you should buy the klm rtw ticket then you can get skyteam points on most of your flights, i dont know to which program you belong but if you belong to flying blue i would fly the following route:

NYC-AMS-JNB with klm
JNB-NBO-BOM with kenya airways
BOM-KUL-HKG with Malaysian
(you should stay a night in hkg because you need to make 3 stops on a rtw)
and then fly HKG-EWR with Continental

And if you are a member of delta or continental frequent flyer programs then i would replace the JNB-NBO-BOM/BOM-KUL-HKG with JNB-DXB-BOM/BOM-DXB-HKG with emirates then you get points for the whole route.

Or could get a normal skyteam rtw:
JFK-AMS-JNB with KL
JNB-CDG with AF(stay a night in Paris because of the 3 stop rule)
CDG-BOM with AF
BOM-ICN-JFK with KE
but with this route you would have to change planes twice in europe and that would add a lot of flying and waiting time to you travel plans.