Right now, my 3 candidates for worst season are 1, 3, and 8.
Season 1 had the problem of trying to find it's footing and isn't really engaging until 10 episodes in. I'd say about half the episodes are enjoyable and the other half is rather forgettable.
Season 3 obviously has the unfortunate handicap of being only 13 episodes, and it certainly doesn't help when almost half of those episodes aren't very good. Granted, I love the other half so I don't think I can put it below Season 1 and say it's the worst season for me.
Then there's Season 8, and I'm sorry everyone, but I'm just not feeling this season so far. We've had a handful of good episodes so far sure, but a lot of them have just been dull, boring, or outright bad, not to mention that the seasonal arc and the inclusion of the Student 6 has been utterly wasted and disappointing so far. Fortunately, there's still half a season left and things could turn around, but from what I saw from the episode that was released this week, it looks like we might be getting more bland storytelling.