It depends on what you're looking for, but I'd definitely go with Great Comet. Plus, Waitress is going to tour and you'll probably have another chance to catch it. With Great Comet, I can't imagine that will be happening.
If you're equally interested in both, Great Comet is not an experience that you could replicate on the road. As great as some of the performances are in Waitress... I'd imagine the touring cast will probably be fairly lovely too.