*comment about Diamond Tiara being worse than both of them*
Really, I think the most evil villain we've had is, indeed, Chrysalis. Including Nightmare Moon, she was simply jealous and spiteful. She had no intentions of physically harming or killing anypony, which I think is a significant fact in showing the extent of which the evil in her made actually allowed; Nightmare Moon was more for severely inconveniencing everyone than outright harming them.
Discord, inconsiderate as he was, has always been more of an anti-villain character than anything. He's not really looking out for either side of the moral code, he's just doing what he finds fun. He's sociopathic and insane, not fully understanding the pain his antics put other ponies through. However, this doesn't truly harm them. Not in any severe ways.
Sombra was probably the worst tyrant of the rulers, ruling over his kingdom with an iron hoof before Celestia and Luna intervened. But at the same time, it's safe to assume he limited his tyrannical insanity to his own land, likely not too heavily intervening in the workings of Equestria in general. I wouldn't be surprised if he'd left all outside the Crystal Empire be.
Chrysalis, however, is a sadistic sociopath. She finds enjoyment and fun in harming the residents that she steals love from, confusing them, watching them wallow in the despair this confusion would cause, laughing as she comes so close to taking down a benevolent duarchy before war could even ensue. She isn't limited to her own kingdom, and while she didn't seem to be a murderer, she was a manipulative brute, feasting on the positive emotions of others not only for nourishment, but for amusement, and finding solace in watching their pain.
Chrysalis is the most evil. And until I learn that Sombra was working his citizens to the bone in order to build a giant mecha that would crush all opposition so he could overthrow neighboring kingdoms that's the argument I'm standing by.