This is like asking me to pick Coen Brother's movie.
I mean, I think I would go with Sweeney Todd... but it might be for sentimental reasons: the recorded Hearn/Lansbury production was my first taste to musical theatre six or seven years ago. It's kind of what made me love musicals. But, that doesn't mean it's not musical theatre story telling at its very finest. Song after song after song just so perfectly driving the characters and plot... never a dull moment in that book or score.
But I digress, I could easily make a case for Sunday in the Park (my #2 of all time), Company (#6 all time) and Follies (#11).
But I'm going with the standard answer (which I guess is a standard for a reason), Sweeney Todd.
"I'm afraid this offer comes off the table... at midnight tonight."
"...maybe the worst bluff I've ever seen."
"Even the members of GOBIAS could agree on that one."