I also have to say season 2, narrowly over season 1. The first two seasons always came across as the most inspired, the most psyched to bring something new to the table (other than pander-y fan service), and with exceptions, the ones packing the most talented writers.
Since then, we've switched story editors four times, with the directors fading in and out, before handing over the reins altogether - and looking back, it really shows. As sentimental as I am to see the show end (and as excited as I am with the "big finale" stuff they seem to be going for), watching them try to pull together all the threads into one vision already shows how much the newer teams couldn't establish one.
We had Megan McCarthy trying to figure out her new direction of "Twilight steps into the role of princess" (the best attempt of the bunch, imo, once it found its footing in season 4), then trying to parlay that into a soon-to-be-pointless "Cutie Map" and a new apprentice for... apprentice things, Josh Haber trying to figure out what he's supposed to do with that and coming up with "have Starlight save the day, one time," Lewis and Songco trying to refocus the lore into a new direction about pillars and shadow ponies (noble attempt, at least), Josh Haber and Nicole Dubac throwing that out in favor of a "friendship school," and now we're told that what it all was actually building towards was getting Twilight ready to take Celestia's job. (Not that season 9, in itself, is worse off than the others in that regard. Supported by them or not, its final season "passing the torch" angle is more straightforward and more possibility-laden than most of them - or so I hope.)
So yeah, season 2 (and 1) all the way. Right now, several fans have an allergic reaction to that answer, because present bias, aka the "so early?!/but we already did that!/bigger=more=better" phenomenon, is a thing. But honestly, this isn't even that close. The later-day seasons were fun sequels, but the first two had the best songs, the most grounded, relatable, and memorable character moments/lines (I'd like to be a tree, 20% cooler, Pinkamena Diane Pieacus... all memes that weren't forgotten in a week) and surprisingly, if you take the time to count them up, the most fan-favorite episodes.
Also, the statistics from the last post do the opposite of prove otherwise, since the picture they paint is of the first two seasons generating increasing hype that peaks going into season 3, then abruptly plateaus.