I liked the seasons 2 and 4.
2 was very authentic as far as I can tell. The really caught the atmosphere of the unions, dock workers etc.
What I liked in season 4 (and part of 5) was how the kids with similar backgrounds ended up. Sometimes a small event changes everything. Randy Wagstaff for example was a happy positive kid who in other circumstances could have become somebody great. In the end he became violent as anybody else.
Namond Brice was so unfitting for the street, he could have ended up dead very soon. It was just a lucky coincidence that Bunny Colvin saved him.
Michael, perhaps the smartest of them all could have become a sportsman, probably he's going to be a killer like Omar.

In season 5 the newspaper events seemed a little forced, it didn't seem organic as the port in season 2. Also, I couldn't really believe how McNulty changed so dramatically from Season 4 to season 5 (returning to cheating and heavy drinking). It looked like a stretch.

In season 3 I liked how the hamsterdam project was executed and later shut down, just for political reasons.

To me the best series ever.