Which low pass frequency filter to configure to measure/calculate DC-DC converter efficiency?
Input voltage is DC and this is dead easy to measure with a DC volt meter. Current into the power supply will be dc plus an amount of AC ripple. The AC part is irrelevant and any old meter reading dc amps will measure average.

The result is: -

DC input voltage multiplied by average input current = input power in watts. 


It is incorrect to measure RMS current because this will give the wrong answer when the input voltage is DC.

Same with the output - if the output voltage is largely DC i.e. it has very little ripple voltage then, output power is: -

DC output voltage multiplied by average current into the load.


Applying a filter makes no sense if you are trying to measure power when one of the consituents of power (namely voltage) is constant dc.

As for using a power meter with a filter, you'll probably find that it won't make much difference which setting you use. Try it and prove it.