Which is a better Groudon?

If you want to max it, 1. If just get it to breakpoints, go with 3.

I would choose the 96%; the 15Atk/15Def is a nice one too, but the difference between the two is basically 1 dodge of a Fast Move to get 1 more Charge Move off. If you care to dodge Fast Moves, then you can get essentially the same output from the 91% as you can from the 96%. Considering how rarely it's going to come down to needing to dodge a single Fast Move to win an overall battle, I'd prefer to just soak that damage and not worry about timing a dodge.

But really, you can't go wrong with any of those Groudons. They're all great.

Optional info MAX CP of each:
1)4052
2)4033
3)4036

2.

Whichever one has Mud shot/Earthquake