Meta: Other important factors to consider are where you are living in Tokyo, your schedule, and how much time you want/have to spend in class. Tokyo is vast, and if you are trying to squeeze a class into a tight schedule, location will make a big difference.
I went to Coto Club in Azabu Juban (a branch of Coto Academy) for a few months. I was very pleased and would definitely recommend it.
The class sizes were small. I think the largest class I had was 6 people. Most were 2 or 3. And there were a number of times where I ended up being the only student. The classes I took were almost completely speaking. The teachers were great and all my classmates were all really nice.
I chose their “Club” location because it was absurdly convenient for me, but it did have the downside of not having many intensive or comprehensive courses. Their primary market seemed to be people with limited schedules, so most of the courses available were of a topical standalone-lesson variety (they called them “part time courses”) where you could miss one and not fall behind. e.g. If your schedule let you attend one of the two class times a week, you wouldn’t be in trouble because the classes didn’t really build on each other, and you would only pay for the classes you planned on attending.
That was pretty cool, and worked really well for what it was, but it wasn’t the type of class I was looking for (I was hoping for a 16-20hr/wk of a more comprehensive nature). I tried to compensate by taking multiple classes simultaneously. That was fun, but the lack of continuity was exhausting. Based on my experience – i.e. the positive of the school itself, and the impracticality of overdosing on smaller classes – if I ever return to Tokyo I would most likely take classes at their Academy location and not look elsewhere.