For WTC, just see the memorial. In May/June, it's starting to be tourist season and the observation deck, museum, etc. will eat up half a day and are only marginally worth it. Trinity church is worth a visit - our daughter goes to their preschool so we sometimes go to services there, but just walking around the cemetary and the chapel are pretty transporting. You're also right by the Oculus (WTC train station) that is cool to see but really it's just a shopping center. If you're with your wife, she might be interested in popping into Century 21 but I would avoid that like the plague.
Also right across from WTC is Brookfield Place if you want to shop and/or grab lunch. There's a PJ Clarke's there that's right on the water with Statue of Liberty Views and yacht docks.
As for the OP mid-town/pre-theater, I'm not as familiar up there, but I will say Carmines is pretty fun and the food is actually damn good. And, Marea, lulz.