Obviously they're all decent and a lot have certain parts or lines that are really good. But for song with the best lyrics overall, Mercy Falls gets taken out of the equation a bit because they are all lyrics relating to the story, and none of them are so amazing in and of themselves to make them the best. They're all good in context but they don't really make for outstanding lyrics for a song - except for One Last Goodbye, as mentioned, just because it is so emotional and doesn't have to relate only to the story.
We won't let you go alone
But we have made a tragic decision,
because your wounds won't heal
It's the final solution
When every day hurts
And tears keep on falling, we're letting you go
The shadows are calling
The Great Escape - As a whole the story told by the lyrics is a great one, the same as Mercy Falls. But I'd say the lyrics themselves are amazing in parts of this song. On the other hand, some parts aren't so great, they are just fairly literal, describing the story lyrics. So yeah, this gets in there because sections of the lyrics are fantastic (especially A New Balance, Aftermath and Dining On Ashes), and the overall story they tell is also amazing.
Shine your light, be the beacon of hope at night
Perfect grace in the barren house of space
Shine your light, blind us when reality bites
Mima, save us from seeing ourselves
Wiseman - Originally I liked almost all other TGE songs better than this, and wasn't that fond of the lyrics either, but now it's one of my favourites, and was the first song I thought of for best SW lyrics, even before TGE. I still don't think the lyrics for the chorus are that great, even knowing the metaphor behind them, but the rest of the lyrics are brilliant. My favourite lines are probably:
What will you do every time your children turn to you?
Wondering when the world is gone, will we go too?
Pieces - The only one of mine so far that hasn't been mentioned already. I think it is similar to Wiseman in its meaning (also in how it is not overly blatant about it), though more emotional and delivered in a darker, more sinister way.
You are watching the world
While she's falling to pieces
But still you smile
And every time your babies cry, you hold them tight
Tell me, how do you sleep at night?