When I was there in Nov last year, I stayed at the Marunouchi Hotel. It is connected to the main railway station by means of an underpass and very handily located.
The limousine bus from the airport stops there (3000 YEN - much much cheaper than the taxis, dont touch them!) and it's a pick up for all the city tours etc.
It was not a raging bargain however, but then no hotels in Tokyo will be.
I understand from my Japanese colleagues (I work for a Japanese company) that it will be decidedly cold there then!!