It depends on whether you're asking which show is best, or which you should see now because you may not get another chance.
I'd rank your three options in this order:
Book of Mormon
Chicago
Waitress (full disclosure: the music I've heard from this show doesn't particularly appeal to me, so I haven't seen it)
If you'll be returning to NY sometime in the relatively near future, you could reverse that order because Waitress will likely close before the other two.
I'll also add my vote to the others who suggested Come From Away and Groundhog Day, both of which I thought were excellent; I'd see either of these before Waitress.
==> this board is a nest of vipers <==
"Michael Riedel...The Perez Hilton of the New York Theatre scene"
- Craig Hepworth, What's On Stage
