In my personal opinion, I think "Sunday" is the best. The song on its own is beautiful, but the manner it which it brings both acts to a close is brilliant, to say the least. He doesn't even use lyrics that are specifically related to the characters and their emotions, and yet I feel it in the song fully and completely.
Honorable mentions to:
Someone in a Tree (Pacific Overtures)
I Wish I Could Forget You (Passion)
Johanna Trio/Quartet (Sweeney Todd)
The Ballad of Booth (Assassins)
Being Alive (objectively. However I prefer Sorry-Grateful on a more personal level)
No More (Into the Woods)
The Miller's Son or Send In the Clowns (Night Music)
Our Time (Merrily)