Considering most factory turbo cars have the MAF's attached to the airbox lid, i'd be inclined to do the same and run the MAF between the filter and the compressor inlet.
The only downside to doing it this way is that if your intake path after the MAF has any leaks, you will possibly over fuel the engine as the MAF is seeing, say, 100% air flow at max load, whereas the engine will only see 90-95% air flow due to losses to atmosphere from leaks...more fuel and less volume of air / positive intake pressure means less torque / power.
You'll drive yourself batshit crazy trying to get it leak free....so might be best to run it in the cold pipe between the intercooler and the throttle body / plenum inlet.
This is why MAP sensors are king....they will always see (near) true engine load at the intake manifold.
What MAF are you running, and most importantly what boost level/s?