We were in Japan 11 days. Four of the days were at the park, 2 in dl and 2 in Disney Sea. We stayed at the Sheraton by the park the 7 days of the trip (got to use our points and only place at that time where we can get four in a room dd,ds and dw) as well as a few days at the Tokyo
Disneyland hotel and the one by Disney Sea Mira Costa.
The Sheraton was close to the monorail, only a few minutes walk from the hotel lobby to the station, then another 5-7 minute ride to park.
The others obviously were more convenient to get to the park, early access and so on.. similar to California DL magic hour (different amount of time of course)... PP, DH, GCH
I'll admit the DL hotels were amazing, but Sheraton wasn't too shabby either and would've gladly pay to stay there. It's just a different vibe in each hotel, all of them spotless and you'll find Japan to be a pretty clean city overall.
To get to Japan, add about thirty minutes from the hotel to a Tokyo station, depending on how bad the train is delayed could be a few more minutes. It's doable, to stay by the park.. but we didn't do the nightlife of Tokyo, Japan as much as family got tired being out all day. So depending on what you want out of your trip, you can be very well insulated of Disney in Japan staying close to the parks.
Have fun on your trip!