Heatsink or IC: how to determine root cause of overtemp?
If I understand correctly, you want to rule out bad thermal contact of BGA with heat sink, right?

If so, consider attach small thermal couple to heat sink fin and bottom of PCB of BGA. As BGA heats up, some heat goes upward to heat sink and some go downard to PCB, depending on thermal resistance of each path. 

The path to PCB is constant. If heatsink path has good/bad thermal contact, the rise/fall time of 2 thermal couples should show difference in rise/fall shape as well as amplitude.

Hope it helps