I’ve been to Yamasa language school in Okazaki (Aichi prefecture) for a three-weeks course a couple of years ago: http://www.yamasa.org/en/. It was really great! For prices, better check their website, but I found it pretty fair back then. You can also get accommodation of various types for your stay through them. I stayed with a host family and this was definitely the best decision. My host parents were very nice, and they also took me on day trips sometimes (the school offers some over the weekends, too) and of course it gives you way more possibilities to chat with “real” Japanese people.
The school offers a variety of courses, depending on what you want to focus on and how long you want to stay. They also changed their program a bit, so take all I say with a grain of salt, as my information might be outdated. I took the SILAC course, which is focused on conversational skills. You can also enhance your main program with e.g. additional private lessons, if you like. In the beginning, there is a placement test to determine which level you are taking. The teachers were great, and my class was really small (between 3-6 people throughout my stay; beginner level classes were a bit larger, but still not large), which makes for a great learning atmosphere.
I can definitely recommend Yamasa, I learned so much, and I would absolutely go there again.