I believe you can do pretty well at $250 a night in Tokyo, although maybe that would be excluding the tax (5% +Y200/night) and service charge (10%) that many major hotels add.

I would guess at that price you can stay at any one of the three main mid-price hotels at Shinjuku: Century Hyatt, Tokyo Hilton, Keio Plaza (now a Summit hotel, I think, whatever that is). If you could find a special rate, you might be able to get into the Westin Ebisu, Imperial (outstanding location for tourism), Okura, or Four Seasons Chinzan-so (the latter a good hotel in a terrible location) -- although probably not at the rates on their website. Email any of these hotels using the name of your company and ask what your "corporate rate" would be -- I bet a number of them would offer you one.