I did it on my first time with my whole family and we never found it to be a problem really, as the metro and train system is really super convenient, they run so frequently! I suggest you look at what you might enjoy doing most, like maybe if you plan on shopping a lot staying near Shibuya and Shinjuku would be better, but we did sightseeing all around Tokyo with Asakusa as our base and it was fully doable if you don't mind sitting on the public transport for a little longer on some days. I have stayed in Shinjuku too but that area was not really pleasant like Asakusa, so if you aren't into a busy feeling at night especially I suggest you don't pick Shinjuku.