Hi Ode
I can't offer you advice on a specific language school, but you are right in that those you mention have something of a mixed reputation.
My partner and I spent a year teaching English in Japan in the early 90s just after completing our respective BAs, so I can give you a few pointers.
First of all, endeavour to learn some Japanese before you go. Even if it is not required by whatever school you work at, you will find it very inconvenient to not speak any. When we went my SO had been able to learn a fair amount of Japanese prior to leaving. Since I was already required to take a year of Latin and a year of Spanish, as well as writing my graduating dissertation (in French).... Japanese did not make it onto my course load. Despite the huge work load it would have added, I sorely regretted not taking Japanese. I did learn some while there, but it was tough going, and Japanese is not one of those languages you can learn easily through osmosis, since it is entirely different, obviously, to the Indo-European language group.
Secondly, if you don't know already, learn to use chopsticks. Apart from the convenience factor, people will appreciate it if you can use Japanese eating implements. Chances are that you will be taken out for many a meal (the Japanese are very hospitable); knowing how to use chopsticks helps to break some of the ice, and shows appreciation of the culture, it is not unlike knowing a language.
Along with being able to use chopsticks, learn to enjoy Japanese food, if you don't already.
When we went to Japan it was easy to pick up teaching work, even without any special teaching certification. That may have changed, however, as this was around 15 years ago.
We basically flew into Tokyo and stayed at a Japanese style inn that caters to foreigners. It is clean, inexpensive, and it has (had?) a bulletin board with job listings and apartments. This is how we found jobs.
The place we stayed at was called the
Kimi Ryokan.
Here is a Frommers review.
As it turned out, we did not select jobs wisely. Based on that experience, here is some advice:
Tempting though it might seem, unless you are
really sure about an employer and the conditions they offer, do not choose a job that comes with a "free apartment." The employer often owns the place, or treats it as such, and they can walk in any time they please.
Be wary of employers who try to discourage you from associating with students outside of class. Some try to do this because they feel that students are receiving "free language lessons," and that they are being denied their cut.

Beyond the obvious annoyance, this is also very isolating because often your students can form the bulk of your social network.
We ended up in a Tokyo bedroom community called Misato.... it was not a pleasant place. On top of that, we only had one day off a week (Sunday) which essentially meant we were stuck in a suburb, with only one day to escape and see something of the country. Given time constraints, we generally fled to Tokyo on Sundays. This meant we were limited in what we were able to see of Japan.
Finally, you should pick up a book on cultural sensitivities. For example... you need to know about bathing. Never, go into a bath without first showering. In Japan baths are for relaxing, not cleaning (that is done in the shower first). Also, never place your chopsticks with the ends pointing downwards into a bowl, this is something only done at funerals. You also need to know that when wearing a yukata (similar to a bathrobe), it is important that you pay attention as to which side folds over which. I can't remember it exactly, but it is different for men and women, and if you do it the wrong way there is an association with burying the dead.
If I remember more I'll post, and if you have any specific questions, also feel free to PM me.