Pantoprazole vs. omeprazole? which is it best for non ulcer dyspepsia? which is safest/less contraindications/side effects?

Depends. : These are the same class of medications and should theoretically work just the same. However different people tend to respond differently to them. You need to do a trial of each and see what makes you feel better (that would be the one that's best for you). It's kind of like what apple is best....depends on what your taste buds like...in this case it's what your dyspepsia likes.