There is not much in the times square area that I would consider to be the top of the list as far as places go. There is a Patsy's there if you really don't want to leave the area. If you don't mind spending about 10 bucks on a cab, Una Pizza Napoletana is my favorite in the city for ultra high temperature Neapolitan style pizza.
While you are in the city it would probably be a good idea to try some classic NY coal oven pizzerias, as that is a style that pretty much only exists in NY. There are a number of them fairly close to you. The Patsy's Harlem location is one of the best, but it might not be the nicest place to visit because of the area that it is in. Instead I would head over to Brooklyn (it might be easier to get to than you think) and try Grimaldi's which is right under the brooklyn bridge, or stay in manhattan and visit one of the Totonno's locations.
John's of bleecker st. (for coal fired) and Joes in the West Village (for a good example of NY street style) are both also pretty close to you, close to each other, and easily accessible by the subway. John's only sells whole pizzas, but you and your wife could split a pizza there and walk right over to Joes to have a slice. I think those two combined with a visit to Una Pizza Napoletana would be the easiest way to try three styles of different, but amazing NY pizza.http://www.johnsbrickovenpizza.com/http://www.totonnos.com/http://www.unapizza.com/http://famousjoespizza.com/http://www.grimaldis.com/http://www.patsyspizzeriany.com/