As of now (which has remained my opinion since season 3 ended), my order from best to worst is...
1, 2, then 3.
Season 1: The only rather weak episode of season 1 was "The Serene Squall. Despite what so many say, I think "The Elysian Kingdom" is a really good episode: it was a lot of fun, and the ending was just so emotional. Very, very solid season, especially for a first season of a show.
Season 2: the duds were "Tomorrow and Tomorrow and Tomorrow" (Christina Chong's performance was the only saving grace of the episode) and "Subspace Rhapsody" (terrible because it's a musical). "Under the Cloak of War" is one of the best episodes of the entire Kurtzman era, so that helps cancel out the absolute disaster that was the musical... otherwise, season 2 would be last for SNW, just for the existence of that episode.
Season 3: overall, definitely the weakest. "Wedding Bell Blues", "A Space Adventure Hour", "Four and a Half Vulcans", and "New Life and New Civilizations" ranged from weak to simply terrible. Just by sheer numbers of weak or bad episodes (4 in one season vs. 3 from two seasons combined), it's a terrible average. Particularly when the seasons are so short, having that many duds is a luxury a series just can't afford to have.
I sincerely hope seasons 4 and 5 are an improvement from season 3. I want SNW to go out on a high note. (Like every other show in the Kurtzman era has managed to do, with the obvious exception of DISCO.)