While I didn't get to watch the show in real time (I'm so sorry, David Simon!), my husband and I enjoyed slow-binge-watching this top-notch quality drama over a four-month period.
Where to begin? I don't think a TV show has ever made me cry as hard as the fourth season finale did. I came to care so much for all the characters, especially the kids, that what happened to Randy, Michael, and Duquan broke my heart. To take four unknown child actors and let them develop and evolve organically was a very gutsy move on TPTB's part. What a satisfying payoff they got in the end! So, yes, season 4 I rank highest.
I may be in the minority here, but I was thoroughly mesmerized by the characters of season 2 as well. It took time at first to get used to the environment/characters so different from those in season 1, but once I got into it, it felt magical. I also like how self-contained the season is.
Seasons 1 and 3 are about the same for me, what with the focus on the Barksdale/Stanfield organizations.
Season 5 was not as bad as some have made it out to be. I'd braced for much worse, so I was pleasantly surprised. The crazy plots did not bother me one bit (as Rinaldo says above, Hamsterdam was equally outrageous), but the Baltimore Sun storyline didn't seem as nuanced as some others, perhaps because Simon himself has admitted to the fact that he felt very strongly about the subject matter. But the final montage just about makes up for whatever was lacking in season 5. I don't think I'd ever seen, nor will I ever see as satisfying a finale as The Wire's.
So it's season 4, 2, 3=1, and 5 -- in that order -- for me. I'd love to hear what everyone else has to say!