I’ve done a short course in Osaka (Namba) at Arc Academy, I think they are in Tokyo too. Most of the schools I think are flexible in terms time. I know that Arc were able to slot me into their ‘intensive’ course for just two weeks even though the course is advertised as a much longer (3 or 6-month) course - I did a test first, and was just put into a group (I think it was level 3 (1~7 levels)) and joined at their current section of the coursework text. Unfortunately it wasnt cheap, I think it was about 40k Yen per week or so, its cheaper to do like 3 months as you want however. You may find cheaper, but I think most schools are expensive and you have to find your own accommodation. Some schools have accommodation deals with local hostels etc, so ask them in advance. That was a few years ago and in Osaka so not sure about Tokyo, maybe some others have more info?