Courtyard Tokyo Station is a couple of blocks from Tokyo Station (Yaesu Entrance), which is where you'll take the train to Kyoto. You can also get buses to and from NRT at the Yaesu side of Tokyo station. In the heat and humidity of August, however, that two block walk can seem like torture (especially with luggage). You might prefer to take a cab than to put your wife and child through that experience.
The Tokyo Station property is much more modern than the Courtyard. I haven't looked at Tripadvisor reviews, but I would expect them to be positive for that reason.
The immediate environs of both properties are meh. But you can walk to restaurants etc. in Ginza from both properties. From the Tokyo Station hotel you can also easily reach the Tokyo Station complex of restaurants etc.

To connect to HND, you could get a cab from Ginza to Hamamatsucho and take the monorail from there. Cab from Tokyo to Hamamatsucho might be a little further, but do-able. *(Or you can get the Yamanote line from Tokyo station).

Overall, I'd lean toward the Courtyard Tokyo Station.