Overall, as shows and their cohesive stories and not singling out any seasons, Breaking Bad is in another league. The writing, for one, is insane. Some scenes feature some of the best dialogue and tense moments on television - "tread lightly". The story itself is genius, insane to the point where it's like a comic book, yet still so believable and tense. The way they portray Walther White's gradual decline in his humanity and morals through the manner in which he acts on screen with his family, his friends and his enemies is great to watch and also allowed Bryan Cranston to give one of the best, of not THE best, television performances, ever. Also, and some may not appreciate this as much, but the attention to detail in the cinematography is stupidly good. Tiny details and elements really tell you about a particular scene, location or character. The framing, colours and visual elements create a stunning style, matched by the shows music. I cannot dissect prison break in as much detail to compare because 1. I can not be bothered, 2. It wasn't that great (for me), but I can understand the appeal, and 3. A lot of it bored me.
I have seen many TV shows. Many. Breaking Bad comes second in my best shows ever list. Prison Break doesn't make the Top 20. But the first season is great, I cannot lie.