First thing you need to ask yourself is how much Japanese you want to learn and how much time you can invest in it.
The second thing is, which kind of Japanese you want to learn? Do you need everyday survival Japanese, or you need to be competent in a business environment? Do you need to do a lot of writing or a lot of speaking?
There are two kinds: group and private lessons.
The advantages for each? With group lessons you can benefit from the structure of a set curriculum and from watching your classmates go through the same material as you. With private lessons it’s all about you and your needs. The class moves at your pace.
The disadvantages? With group lessons you’re stuck with a certain rhythm and the class schedule tends to be inflexible. You also get less attention from the teacher (depending on the class size). The main issue with private lessons is that they are considerably more expensive, and because you decide when they happen, it’s easy to let them slip and not keep up with your studies.
Are you ready to commit to a weekly schedule? If you can, it will be cheaper and the classes will keep you on your toes.
If your job or routine throws curve balls at you every once in a while, you might want to ask about flexible class schedules. Many schools offer cancellation policies or will let you join a different class to make up for the one you lost. Overall, private lessons offer more flexibility regarding scheduling.
This one is a bit obvious, but make sure the school is within your budget. Furthermore, ask about tuition payment plans. Some schools offer monthly payments, others offer a discount if you pay in advance, while others sell sets of ten or more coupons that you can use within a specified time to take classes.
AJALT (Roppongi): Customizable lessons with instructors who are specialists in business or diplomatic Japanese. Small classrooms and they make their own textbooks.
ARC Academy Japanese Language School (Shinjuku): Small group lessons, multicultural classrooms, helpful staff, and after-hours help.
Academy of Language Arts (Iidabashi): Group and Individual lessons at all levels. You can prepare Japanese proficiency exams, improve writing skills or your listening skills.
Ofin (Akasaka): Small classes, weekends available, private courses as well as workshops such as calligraphy or "SUMIE" (Japanese ink painting).