I was going to say The Last Ship for Best Musical since I personally liked it far better than more likely nominees An American in Paris and The Visit. But since others already came in with that, I'll say:
Judy Kuhn in Fun Home. It's likely that she'll get it, but my fear is that there may just be so much competition in that category from within her own show that she somehow gets left out, and I think she's just doing extraordinary work in Fun Home. Honestly, I'd love to see Kuhn, Lucas, and Skeggs all get in with a Lead Actress nod for Malone.