If you are running that close to the limit, then the case temp may not be good enough. In a BGA package, most of the heat goes into the PCB (through the balls). Therefore, it is often better to try to use ThetaJ-B (Junction-to-Board) versus ThetaJ-C (Junction-to-Case). Note: If you do use ThetaJ-B, you must get your thermocouple right next to the package (virtually touching) to get an accurate measurement.
Technically, there is another factor, PhiJ-B, that may be more appropriate to your situation. It depends on your system, i.e. system exposed to open enviornment with air movement, system in enclosure with minimal air movement / no appreciable cooling of the flowing air, circuit connected to a large ground plane (a.k.a. huge heat sink / spreader :-D), etc..
The best method for estimating die temp is to use the method outlined by IRSTUFF. I have used that method successfully in the past, and found it be VERY accurate (ran a correlation exercise with the component manufacturer and the correlation factor was like 98%). Furthermore, it makes the most sense. You are measuring a property on the actual die that is linear over temperature. Plus you don't have to worry about the thermal lagging / smoothing effect of the case and/or PCB.