YahooBB is one option.

http://www.bbapply.com/

Another which I prefer is NTT's B-Flets service.

http://www.ntt-east.co.jp/product_e/05/index.html

The cost of getting a phone line is Japan is dramatically cheaper than even a few years ago so I would inquire of potential landlords whether a contract for a line can be set up directly by the tenant with the phone company or whether you will be using a line running through a PBX for the building. Most likely they will ask that you make arrangements for your own line. Easy as calling NTT and making an appointment.

Mike