I think it depends on what the ECU does with the temperature reading. If it uses a factor to correct temperature for boost, then after the water injection and before the turbo. If it uses straight temperature, it seems like the most consistent readings would come from having the IAT (Intake Air Temp) located at the throttle body.
I don't have experience with water injection or aftermarket ECUs, so I'm just guessing here.
__________________
|