If it works out, I'd do a split stay between Tokyo Bay and Ueno, I think it takes around 30 minutes to make the trip - less if on an express.
However this didn't work out for us, as we'd need 1 night in central Tokyo, then 4 nights at Tokyo Bay, then returning to Central Tokyo for another 4 nights, then off to Osaka for 5 nights, and we don't like hotel hopping, so we decided to stay in Shinjuku for the Tokyo section of the trip, and make daily trips to TDL. We will be faced with the long early morning train rides, but hey, I figured it's part of the "Japan" Experience!
Having said that, if a Disney owned hotel comes up super cheap, we may still consider a couple of nights there
The Disney owned hotels are very expensive, but there are several others located very close at Tokyo Bay which would be just as good, but without the Disney themeing. Look into either the Hilton Tokyo Bay or the Sheraton,
I looked into Ryokans, and while some of them look nice I decided that you don't get much for the price you pay. I
must have a private bathroom, and a lot of them don't have this option, unless you're willing to pay extra, and a hotel ended up being a better option, less of the "Japan" Experience, that I mentioned previously, but to me, private bathrooms are more important then having that experience