This is tough. Personally, I think Betsy Wolfe's performance in Waitress is a must-see. She embodies Jenna so brilliantly, and I was particularly moved by her. Now granted, Betsy is one of my favorite Broadway actresses, but even if she wasn't, I think her performance in this show would turn me into a fan.
On the other hand, Waitress is going on tour, whereas Kinky Boots seems to be on the last legs of its Broadway run. It is truly a spectacular production, and as others have stated, J. Harrison Ghee is just BRILLIANT (saw him when he was on the tour). Plus the show has a wonderful message.
Personally, if you haven't seen either, I would go with Kinky Boots, but you really couldn't go wrong either way.