If you're spending three to four days at Disney Resort, I would recommend changing hotels while in Tokyo. Stay at one in "central" Tokyo for the "Tokyo" part of the trip and stay at one on the monorail line at Tokyo Bay for the "Disney" part of the trip.
Commuting to and from Tokyo Disney each day is certainly doable. But, it can still take a lot of time (e.g. up to an hour). And when you need to be at the parks an hour early and stay until closing (or really, after closing doing shopping), they can be LONG days. On our first two trips, we commuted each day, and we'd often end up only getting around 5/6 hours sleep each night. On our most recent trip we stayed at the Hilton at Tokyo Bay and it was so much better. We even ducked back to the hotel one day when the weather turned unexpectedly cold and wet to grab appropriate jackets.