I think season 4 is considered hands down the best season by critics and most viewers. The only downside is that besides John Lithgow, there's not a lot going on. That storyline is obviously an incredible one, and probably the best in the series, but the side stories of everyone else in the department are pretty terrible. Season 7 has all good side stories, too. I put them on three different tiers like so:
4, 7
1, 2, 6 (I liked 6, even though it got pretty cheesy at times)
3, 5