If you were simply overnighting in Tokyo before an early flight out of HND, I think Shinagawa is fine, but it's a bit dull for two days IMO. As an alternative, I suggest somewhere close to an Asakusa Line station like Shimbashi, Higashi Ginza, Nihonbashi, or even Asakusa, which are walkable neighbourhoods that I prefer to Shinagawa. YMMV:
https://en.wikipedia.org/wiki/Toei_Asakusa_Line

You can get an airport train from the Asakusa line platforms. (But beware, not all trains on the line go to HND, so make sure you get an airport train).