There are actually more hotels offering triple rooms than you thought. Don't expect pple do research for you... Go open Google map and look at the area around the train stations. Look out for the hotel icon and click on them to get the brief description and user submitted pictures. Click on the hotel link and look at the rooms they have. It usually link to their Japanese website but major hotels got English language button. Even if no English language, just mouse over the links and go to their accomodation / room page to see what kind of rooms they have. If they do have triple rooms, take note of the name and try to find the hotel in third party sites like rakuten or japanican (if agoda or booking.com don't have).
Its very tedious but you may end up finding a hotel that fits your needs, instead of waiting here for replies.
Do note that some hotels only release rooms 3-6mths in advance, so if you are desperate you can email them to check if they are really fully booked or they haven't release the rooms for online booking.
