Couple of options might be;
Shinjuku. West side of the station has Yodobashi Camera, which carries JDM models of Seiko, Citizen and the like (quite a nice display). There's a big BIC Camera at the west exit also. On the same side is GMT, and north of the station os Ippukishi, BEST etc (although maybe not as good for JDM). Advantage is that being Shinjuku there's loads of things to do with a three year old!
Ginza. Primarily the Seiko store between Yurakucho and Ginza itself, is good to see. If you're in Ginza the Nissan Crossing has a very cool car there at the moment (like something futuristic from Gran Turismo), and recommend Cafe Miyukikan too for a stop. More on the watch front, Watch CTI in Ginza 1-chome often has some nice pieces. All of those are within a few minutes walk of each other (and Lemon-sha is just round the corner from Watch CTI.
Ueno. Mizutani is a good shop for a range of Seiko although you never quite know what you will get, and there's another shop at the south end of the same street. Mizutani is just south of the station exit (cross the main road and go left into Ameyayokocho area). You're very close to Ueno Park, which is nice to walk around, as well as Shinobazu pond which might be nice.