Without giving it too much thought, I'd say DS9 season 6 or TOS season 1, with DS9 season 4 also being a contender.
DS9 season 6 opened with the franchise's first example of long-form storytelling, with "Rocks and Shoals" being a standout episode in that arc. It also gave us classics like "Far Beyond the Stars" and "In the Pale Moonlight". Overall the episodes were solid with few duds.
Similarly season 4 also opened strongly, with four of the first five episodes all being strong, with "The Visitor" among the franchise's best ever instalments and "Rejoined" also being very very good. ("Indiscretion" isn't as good as the first three or fifth episode.) It also features "Homefront"/"Paradise Lost". Granted, the second half of season 4 probably isn't quite as strong as the first half.
TOS season 1 established so much of the template of what Star Trek is, and many of the episodes still hold up very well even close to 60 years later, including "The Cage"/"The Menagerie", "Where No Man Has Gone Before", "Balance of Terror", "The Galileo Seven", "Space Seed", "The Devil in the Dark" and, of course, "City on the Edge of Forever".
ENT season 4 definitely gets the prize for "most improved" season. (Yes, I have seen PIC season 3, but don't rate it as highly as most people.)
PRO season 1 gets the prize for best debut season after TOS. I think it did a great job in putting a new spin on the franchise while telling good, family-friendly stories that developed both plot and characters.