Is a motor-generator set a reasonable way to get the purest waveform electricity?
The "purest waveform" you want for noise-sensitive equipment is flat DC. 

The both simplest and best way to get it is a battery. Why?

Any kind of AC needs rectification of some kind. Even a motor-generator with a standard DC generator produces a rectified sinusoidal current. You could use an unipolar DC generator, as it was done for ultra-low-voltage ultra-high-current DC applications as galvanic plating in the past.

But even then, you have a second concern, and that's AC currents on ground. In your motor-generator the two machines are connected with a steel rod. It's not possible not to have at least some AC noise on the DC ground without replacing that one by glass fibre or something like that.

Use a battery. Charge it if the device is not used. Medical equipment is sometimes designed that way. (It makes also the compliance testing simpler.)