Yes, in Tokyo you have lots of choices as far as accommodation is concerned, but finding one suited you may not be so easy. Most travelers will use the public transportation system to get around, so finding a hotel near a Metro station is preferable. I prefer hotel which has good service, good wifi connection, and good accessibility, BellClassic Hotel seems fitting my bill.
The hotel is only one minute walk to Otsuka JR station, Otsuka is only 10 minutes walk, or 1 Metro stop away to Ikebukuro. Buy a 750 Yen JR day pass, you can go anywhere in Tokyo. Direct airport connection available in Shinjuku and Nippori , both are on JR Yamanoto Line.
It is a large hotel with over 150 rooms, The hotel lobby is modern and bright, clean and spacious, the Japanese management look after the place well. They are efficient but strict! Most staffs do not speak English, they do not allow check in before 2 pm, I arrive at 1.30 pm and was made to sit in the lobby and wait. The hotel are mainly geared for local businessmen, and there are conference to be held daily. If you want to be away from your noisy fellow foreign tourists, this is the place for you.
The room size is average, but everything from good wifi connection, good TV reception (no English channels), tea making facilities, even toothbrush are available.
The cost to stay in this solid four star hotel is only US$60 per night in a single room, which is cheaper and more comfortable in those cramped stuffy hostels and inns in Shinjuku.