There are countless hotels in Tokyo, and if you don't need luxury but will settle for a plain but serviceable room, then the list is almost infinite.
Depending on what your wife wants to shop for, Ginza may or may not be the best place to stay.
I suggest getting a Tokyo city guidebook, figuring out which part of the city you want to stay in (although the excellent public transit system makes this less of an issue than in some cities), finding out which hotels in your preferred price range are there, and then going to the websites of the hotels on your short list to determine which one to go to.
If you want luxury, that's certainly available. If all you want is a place to lay your heads at night and take a shower in the morning, there are literally hundreds of clean and safe options available.