I guess that depends on where you plan to visit in Tokyo and how old your children are. I would want to avoid changing hotels to eliminate packing and unpacking. But I would also want to avoid rush hour train rides and changing trains multiple times with small children.
Many hotels around Disney seem to offer "family" type rooms, so you can all stay in 1 room. I also liked Oriental Hotel Tokyo Bay for the convenience. There is a covered walkway to Shin-Urayasu station, and they say the train ride to Tokyo station only takes 17 min. There is a shopping mall and AEON next to the station too.
We stayed in a small regular room because it was just me and my daughter, but they have rooms called "Baby Sweet" and "Kiddy Sweet" that are designed for stays with babies and small children. There should be a small laundry room on the lobby floor. I did not check it out, as we didn't need it. 24-hour open Lawson convenience store inside the hotel was great.
Hope you will find the accommodations that meet your needs!