Do not know when was last time you were at Shinagawa, but around Shinagawa station is changing a lot.

As some has mentioned, no matter what part of Tokyo you decide to stay it is likely be 11:00 p.m. – 11:30 p.m. once you settle in at a hotel. Then next morning Narita Express no. 11 departs Shinjuku at 8:02 a.m., Shinagawa at 8:19 a.m., and Tokyo at 8:30 a.m. I do not think there will be a lot of time to wonder around if you want good night sleep.

If you need a hotel room only for three to four hours of sleep then why bother with Intercontinental Strings? Cheaper business hotels may be what will work for you especially if all you have is a backpack.

Is wondering around in Tokyo must? If I were in your situation I will simply get a room at a hotel at Haneda International Terminal and take Limousine Bus from Haneda Airport to Narita Airport next morning. The hotel is right at the terminal, a hotel restaurant opens till 1 a.m. and there are two or three restaurants in the terminal pre-security area which open 24 hrs. There is also a convenience store at an International Terminal which opens 24 hrs.