Hmm, this is a difficult choice! Season 1 is easy, with Lethe being the only one not bogged down by the ongoing nonsense, and even better that it managed to really justify the familial connection and did it in a way that I found additive rather than reductive. Sarek, Burnham, and even Spock (despite never appearing) were enriched as characters by that episode.
While I liked Season 2 leagues more than Season 1, the nature of the continuing story (especially once it kicked into gear after Light and Shadows) makes it hard to separate them. I think An Obol for Charon wins as best in the season, due to the sphere plot being a good concept as well as for the scenes between Saru and Burnham. Runner-up would be Such Sweet Sorrow, Part 1 (even though Part 2 failing to stick the landing diminishes the impact a bit in retrospect). I'm surprised to see Light and Shadows and If Memory Serves so fondly remembered, as for me those were the lowest in the season.