Here's a blog to discuss, among other things, whether comics are canon or not.
Andy Price said that it's up to us to decide whether the comics are canon or not. However, someone said that he also said Hasbro considers them canon unless contradicted by the show (what, so they don't have the power to make sure the show doesn't contradict the comics? The writers must have all the power now. If Hasbro doesn't have that kind of power, then is their word really WordOfGod?).
Here's the thing. Although I do like the comics, I want them to be non-canon. Well, the Heather Nuhfer ones definitely are since the Nightmare Rarity arc was contradicted by the show (since Princess Twilight Sparkle shows the Nightmare Moon transformation/possession happening very differently from the comics). But the Katie Cook ones do try to fit in, but I'm sure you already know the reason I want the comics to be non-canon.
Queen Chrysalis. She is a dark, menacing, sinister, creepy villain, and, despite being my favorite villain, what she did to Twilight at the end of A Canterlot Wedding Part 1 (turning all her friends, brother, and mentor against her without even corrupting any of them except maybe Shining Armor), she must die for that. She should have fallen to her doom after Shining Armor and Cadance blasted her over the edge of Canterlot (high up a mountain), besides her episodes are Disney quality and many villains fall to their deaths.
Of course the comics depict her survival, why? Because most of the fandom loved her too much to want her to be dead and she was a fan-favorite villain. Bringing Chrysalis back was a form of fanservice. For the "fitting in" part, Meghan never mentioned Chrysalis after the episodes (unlike Sombra). The comics make her even darker than in the show, which is quite an achievement, but she survives her fight with Twilight. She even escapes her imprisonment and ends up karma houdini after being even more evil than the show's Sombra (in contrast, the comics' Sombra is more sympathetic and reforms).
So, do you view the comics as canon or not? After what Hasbro apparently said are we allowed to view the comics as non-canon?
Edit: They have been declared canon but in their own separate universe. Count them like the alternate realities of Spider-Man Secret Wars