I would say Season 2. Season 3 definitely had some great episodes, but at half the length and with that constant feeling of doom in the air as to whether that meant the end, it couldn't quite match up. It also helped that I joined the fandom just after Season 1 finished airing, so Season 2 was the first one I saw unfold episode-by-episode, and it was when I really started to join in with the community. So, I kinda prefer it due to personal, external factors, more than anything. Had Season 3 been full-length, I might have had that contending more.
Truth be told, all of the seasons had their charm for me; there's none I'd really say were especially bad compared to the others. Season 2 just hit that sweet spot, although with what the creators have divulged thus far, Season 4 may well be able to knock that off the top spot...