How do I calculate propeller effects on pitching moment?
The propeller causes pitching (and yawing) moments. There are two main reasons for that:

1) flow change around the fuselage (and central wing and tail)
2) thrust change. 

Thrust change is simpler to grasp and estimate. The thrust vector will cause a moment, because (90% of the time) it's a bit tilted and does not pass through the CG of the aircraft.

Several model aircraft have intentionally tilted propeller / motors. The perfect amount of tilt is found through flight tests, because its simpler and more accurate to try and feel the effect. 

A pusher configuration has quite similar concerns related to thrust vector, however the flow change effect is much less than a tractor configuration. This is because for the pusher configuration the accelerated flow does not effect the air vehicle any more.

Calculation of these effects range from hand calculations (spreadsheets) to CFD and finally to flight tests (where you'd do controlled tests to derive the model parameters).

For RC aircraft I'd suggest following the rule of thumbs that have been established in the RC communities.

Finally, tractor / pusher configuration selection should be based on several other factors and thrust moment is probably not the most important one.