Hmmm..... you'd need to hook up with an electrical contractor that has a power quality analyzer. The average electrical contractor does not own this equipment, but one that does mostly commercial work does. It's a high-dollar piece. This measures several things related to the power output, with the "purity" of the waveform being among them. You'll pay at least a few hundred bucks for such a test. Measuring the power quality while the genset is partially and fully loaded should be part of the testing procedure.
I think that it is important to realize that the typical generator sold for home backup power is not intended to provide the cleanest of power. That being said, I believe that it is safe to say that home genset power is at least as clean or possibly cleaner than your local utilities's power. Having done hundreds of power quality studies, utility power is no where as "clean" as people might want to believe that it is.
Now, on to your furnace... the boards in HVAC equipment are fairly bulletproof. They are engineered to such wide tolerances, that they will readily tolerate wide fluctuations in the voltage and frequency of the input power. They will all tolerate voltages and frequencies +- 10% with no trouble. But, if you're considering operating your computer or stereo equipment on a genset, forget it. This type of electronic equipment demands power that's dead nuts nominal most of the time. While I hold to my basic belief that most gensets are at least as clean as utility power, I wouldn't bet the farm on it. As far as generators go, I've only personally done power quality studies on a few larger 6 and 8 cyl gensets. I'm not sure what you might be getting out of the more common Tescumseh/Briggs/Honda type generators. Most of the "whole house" type large gensets will have meters that show the voltage and frequency on each phase. While this may not show how "choppy" the waveform is, it can be a pretty good indicator of decent power.