Firstly - what are you trying to measure? I'm guessing the speed of rotation.
It may well be that Hall effect switches are the best option as they should be able to detect the magnets from a safe distance, failing that a simple inductive pick-up pf a few turns of wire should induce enough voltage that it can be filtered and used to measure frequency. If you want to do it optically, a scanner is probably the least appropriate technology because your would be periodically checking a moving object and strobing is likely. A better optical method would be to fix a small mirror or reflective tape to the rotor and shine an IR LED at it. Use an IR detector to look for flashes reflected from the mirror. Do not use a remote control type of IR receiver as these will only respond to modulated carriers, the kind you want are simple IR photo-detectors.
Brian.