This is the only upmarket accommodation in Shinjuku that seems to assume its guests will actually be getting around by public transport – it's just steps from Shinjuku Station's south exit. The hotel occupies the 20th to 35th floors, so the rooms (spacious with big beds) have views over Shinjuku. If you can lock in a good rate, this is a great deal.
Hotel Century Southern Tower
Shinjuku & Northwest Tokyo