It depends, although I am leaning towards Earthquake. Thunder Punch already has Flying types covered, and Stone Edge doesn't really hit anything other than Bug types which are uncommon and STAB Fire Punch has them covered anyway.
Stone Edge may be a better way of dispatching Flying types though, as often Thunder Punch is a 2HKO.
Earthquake is just a generally good coverage move, hitting Electrig types super effectively, and is powerful and reliable.
As I said, it depends, but I would go for Earthquake for reliability and coverage.
Hope I helped