For me it's season 4 of TNG. It's the season I grew up watching on repeat. I like every episode which is rare for an entire season. It also has a great verity of episodes. You get a good amount of sci fi, mystery, political intrigue, and the thing season 4 is most known for, deep character development. Best episode for me has to be a tie between Drumhead and The Wounded, but I also have a soft spot for Future Imperfect.
My top 3 and it's a really close call:
DS9: 4
TOS: 1
TNG: 3
TOS was unconventional in 1966 with cast and mature themes. Not just Kirk wanting to shag everything in space, but plot content and ideas being mature (e.g. something a 8 year-old won't connect with.) Twilight Zone and Outer Limits may be as much strong influences as Bonanza and Forbidden Planet, but the show went in its own original direction, and brought much interesting philosophizing on the human condition.
TNG season 3 for me right now. I'm still floored by all the production problems, yet the new tone and feel and storytelling put TNG into its own class of show. (A fan of season 2, which was already on the right road, season 3 only refined the best of 2 and ditched the remaining comedy stuff as well as revising the captain's log format since, by 1988, enough people had VCRs that they didn't need commercial break recaps incessantly, but kept the log idea in use in more refined ways.)
DS9 was solid, but needed a revitalization and new purpose and does it ever deliver... It's the only show that could dare do something big as ending the Klingon peace treaty. Never mind the Dominion and Maquis. DS9, in many ways, is the spiritual successor of TOS that TNG could never be, what with a return to unknown space exploration, the edge of another wild frontier, an enemy risking war, the occasional nutty command figure... and DS9 did dare to face off some big philosophical stuff without the kid gloves that TNG and TOS had. Sisko did things for the greater good, especially in later seasons (and a few things early on, like taking punishment for the crew that even Kirk wouldn't do and he'd be the only other one to do it (e.g. "The Gamesters of Triskeleon", another underrated gem!)). He accommodated everyone while demanding a middle ground. He even fought fire with fire when no absolutely other option was viable*. He was doing the dirty work to save the Federation all while Picard and others just talked pretty and with the added benefit of how scripts could tidily by the end of the episode, also known as "The Brady Bunch Rule". Yeah, I did start digressing around season 4, but DS9 is the most mature Trek of them all... it's always going to be high on my list.
* and those episodes are an inversion of older Trek, where the Captain would otherwise order something controversial but the crew all pounce because Captain is under alien influence or whatever. DS9 inverted this scenario with mesmerizing depth.
This order could change again by tomorrow, then the next day, the day after, etc... TNG 3
is incredibly good - the last season before repetitiveness and rut step in (e.g. more family shlock, character drama steering too much into soap opera, many returning characters for sequels, etc. That said, a bunch of season 4 does hold up and it is TNG's final great season.)