I voted 3rd best.
I'm torn for best, but I'll say S2, because it started as the spy drama we had known, then turned on its head mid-season and became a different monster that I thoroughly enjoyed. The cliffhanger was ok, but you couldn't see it coming. I did like everything that led up to that moment.
S1 second because it was the spy drama that I began to enjoy that pulled me into the entire thing. Again, it started as one thing, then everything changed and there was one clear threat to SD-6, the Man. The cliffhanger was killer.
S4 is third on the list. It started rough, no connection, and questions piling on top of each other. Finally, it all starts to come together and I was mostly satisifed with it. There are still questions out there that I don't have the answers to besides the cliffhanger, but there should always be questions. I think they learned from mistakes in the 3rd season, and rather than pound the questions repeatedly into my head, they 'abandoned' the questions until something new would be revealed. It was almost too much, and I had to remind myself what questions had been posed at times. There was no continuing enemy presence throughout the season, I mean there was Clone and Elena, but I never really felt like they were there, the priority of APO, again and again. I like the cliffhanger: nothing changes in the Syd/Vaughn relationship, but its beginnings are now murky.
S3 is fourth, but it's not this "I wish it never happened" season that others have. I do like that they tied bits from the 3rd into the 4th, because you have to acknowledge that the season happened. The beginning was dull, questions were pounded into me again and again without significant gain (amnesia, Passenger). It meandered, but at least it had the consistent enemy of the Covenant/Sark. The cliffhanger was a letdown, (good set-up, poor execution) as I don't like the answer to the question posed; it seemed like something directly pertaining to Syd should have been the answer, like a version of Project Christmas or along those lines. It was a bland season, but it was still better than most other seasons of other shows out there.
However, that's not nearly as bad as the logic, pacing, and character flaws of the 3rd season. Meanwhile, the 1st 2 seasons managed to bring the drama home without sacrificing verisimilitude. 
