Perhaps the most challenging components to thermocouple are BGAs, since the area of reflow is hidden underneath the component. The most accurate methodologies are destructive. The simplest way to thermocouple a BGA may be to drill a hole on the underside of the BGA and thread the TC bead into the drill-out hole that allows access to the target area without having to remove and re-attach the BGA.
Another method is to use a very thin gauge TC wire (40 AWG) and separate the two dissimilar wires, as shown below. Then attach the TC and place the BGA on top of the TCs. Again, the point of this exercise is to achieve an accurate “direct” reading.

Special thanks to Scott Nelson at Harris Corporation for providing this example.
A non-destructive method for thermocoupling BGAs is to simply mount the TC on top of the BGA and, perhaps, to the underside of the PCB directly below the BGA, and develop an offset. There is no right or wrong answer; much depends on your production tolerances and a whole host of other variables that have been discussed in this guide. The point is that only you know your process and limitations with respect to product and tools.
Note: This is an area of particular interest to me since it is a concern that just about everyone has an opinion on and no true right or wrong way has been developed. Stay tuned more to come soon.
TCs are sensitive instruments of measurement. TCs are abused mainly because they are misunderstood. First, go out and purchase a set of TCs with the proper rating for your process with the least amount of variability. Look at the thermocouples that you are using. Organize the TCs according to observed temperature values by plugging them into your profiler. For now, we are not going to enter into a discussion about electromotive force, thermometric sensitivity, linear vs. non-linear, TC conductor length, weld type, or even conductor material. What we are looking for here is that we are dealing with Type “K” thermocouples.