Is it feasible to go to Ooedo-Onsen Monogatari in Odaiba after HND arrival? Take the subway there from 11pm and stay until morning. It seems interesting as a place to relax.
Sure - It's feasible, but check the onsen website to make sure that your visit doesn't coincide with the monthly maintenance days when the onsen closes.
If you depart HND at 11:00pm, the shuttle bus won't be operating by the time you get to Shinagawa or Tokyo Teleport:
http://daiba.ooedoonsen.jp/access/im...-modal-5-2.jpg
The onsen is open until 9:00am next day. (Last entry at 7:00)
If you want to use public transit, as much as possible, you could either
(1) Take monorail to Tennozu Isle, then JR Rinkai Line to Tokyo Teleport. Then find a cab at Tokyo Teleport to take you to the the onsen. I feel pretty confident you'll get a cab there ...
or
(2) Take the 23:09 Keikyu line local train to Shimbashi. Change there to Yurikamome line. Get off at Telecom Center station and walk.
The first free shuttle bus from the onsen to Shinagawa next morning is at 8:15 am. If you need to be back at HND earlier, you'll need to take the reverse of (1) or (2) above.