Which Rhydon to power up?

2, first one already at high level.

There is no debate, MS/EQ deals about 10% more damage against a pure electric type than MS/SE. Super effectiveness matters a lot.

No need to power up the one at L31 already though. Spend your stardust to get number 2 to level 30.

Earthquake and Stone Edge present different opportunities for Rhydon.

With Stone Edge, he performs well as a generalist as, coupled with Mud Slap, he has a wide variety of type coverage, including the ability to take on flying types. With Earthquake however, he is the strongest ground attacker in the game so far and is the better choice if the typing is in your favour, e.g. versus plain electric or fire types.

As 333-blue said though, option 1 is already sufficiently developed. Option 2 is worth doing if you can spare the stardust.