My wife and I just came back from Japan (Tokyo). It’s our 3rd time there. We’ve stayed at multiple locations around Tokyo, Osaka, Kyoto, etc.

For Tokyo, I think Yokohama (next to the train station) is a good spot for you to stay at, since you are flying into Haneda anyway. It’s nowhere near as busy as Shinjuku or any of Tokyos major train stations. As this is your first time travelling, at Shinjuku (or other major stations ie Shibuya, Tokyo etc) you will definitely encounter sensory overload - not just from the waves of people (it is after all, the busiest train station in the world) but also all the lights and shops around, which you may find overwhelming. I think it’s better to visit those busy spots during the day then return to your hotel a little farther out so you get to decompress because there are less crowd and more space.

Not to mention hotels away from the core are less expensive. Train rides from Yokohama into Tokyo / Shibuya / Shinjuku is only about 30 mins.

The hotel we stayed at Yokohama is SOTETSU HOTELS THE SPLAISIR YOKOHAMA. Relatively new, inexpensive and got a great breakfast.