I love Living Witness, but I'm finally going to vote for it. It's a blast seeing the crew in a totally evil vein (VOY's version of Breaking Bad? Hmm...) It also showed how easily history can be built on misinformation.
Timeless for me though is a very emotional story, which wins it for me. Tortured Harry in one episode has more gravitas than normal Harry had in the rest of the show. He's desperate to make things right at any cost. Things are reset at the end, obviously, but Harry receiving a message from himself was the perfect ending.
Of course they tried to rip off the story with Endgame, which was nowhere near the same level.
Living Witness - 3
Timeless - 3