Becker.
Kudos to Edberg - if you're gonna have a 10-25 record vs. a rival, having your 10 wins encompass a 3-1 Slam record (including two finals), plus a Masters (YEC) win is the way to have that losing record. Nice, quality, big-stage wins.
But, remember Davis Cup was a huge deal back then too, a big stage, and Becker beat Edberg 3 times in Davis Cup (including a couple absolute beatdowns) and has, I think, a WCT win over Edberg (another event that was a big deal back then).
So, the "biggest stages wins" are fairly equal. True, the Slam stage is the biggest and Edberg leads 3-1, but with Becker's own big stage wins plus the very fact of a 25-10 dominant record, I think he "wins" the rivalry fairly clearly.
I was always surprised they didn't play at least a few more times in Slams.