You can make a case for 3 as the ultimate Wire Season, because it is the most Wire season. It has the biggest, best gangland storyline that gives you both the Barksdales and Stanfields. The formation of the Co-op, bringing an increased role for Prop Joe and the incredible comic gift that is the Robert's Rules of Order along with it. It has the MCU in full effect, Carcetti and the mayor coming into focus, the best McNulty arc, the best of Bunny Colvin, the best of Stringer and Avon, the best of Omar, the best of Cutty, the best of Bunk*, the incredible off-handed reveal about Rawls, the gutpunch of the turn Prez's story takes. It has all of the most striking elements of the show except the kids.
Season 4, on the other hand, is fantastic and absolutely worthy of being in the discussion of the best season of TV ever. But it is missing a lot of the elements that define the show when you think back on it. In an abundance of caution, I will spoilertag:
Warning: Spoiler! (Click to show)
Can it really be the best season of the show when so many of its strongest characters are either entirely out of the picture (Stringer, Avon) or marginalized (McNulty, Daniels, Bodie despite how powerful the ending is) or dealing with less interesting material (Omar, Cutty) than they have been given in the past?
Sure it can, because so much of the rest of it is so incredibly strong that none of those people need to take the reins. And it is a great season for Prez, Bunny, Carver, Prop Joe, and of course the kids. But no Barksdales, no focused MCU investigation, and very little McNulty make 4 feel less representative of the show as a whole. It's very much latter-day The Wire, whereas 3 acts as a perfect bridge between the Barksdale and Stansfield eras, and gets to live in both worlds simultaneously.
Also, this is a great thread topic, but come on people. If you can't muster more than one sentence on what makes an entire season of television great, why bother?
*Okay, the Bunk is elementally, unfailingly awesome at each and every moment. But his tearing into Omar is the best work Wendell Pierce does in the entire series.