My advice is - if you are unsure about the reliability of your temp. readings, then trying using a laser based thermometer and take readings from the top of the heat sink itself or directly from the CPU's thermal spreader if you can get a clear line of sight with the laser.
For me - I use a combination of BIOS measurements and 3rd party tools - they're very, very close in readings, so it that's good enough for me (as I'm not pushing my CPU to its thermal limits).
Do some reading on the temp. variations though and you'll see there can be quite a bit of variation between tools. Look at what tools are most highly recommended by others and stick with those.