Jib71's suggestions seems the best.

Are you on a layover or will you be venturing back to Tokyo the next day? If you're staying in town for a few days, then you have some other options hotels with onsen further from the airport like the Dormy Inns.

Here's three spas open at midnight in Tokyo http://jp-hotnow.com/en/detail/jphn_...egory=wellness and there's a few more in Yokohama like Manyo Club or Spa Eas which would be quite a commute. You could take the Haneda Friendly Limo to Ikebukuro's Spa Resta if you find the rail & metro system more than you want to tackle after a long flight.

Personally, for something near Haneda, I'd probably stay in a business class hotel room with a bath tub and save the cash for a ryokan or super sento experience instead.

Tokyu Stay also opened a hotel in Kamata last year and they're still offering opening specials of 5,580 - 6,900 JPY/night for a B type single occupancy room with bathtub in Feb-March. It's connected by the Keikyu Airport Line to Keikyukamata Station
Schedule:
http://www.hyperdia.com/en/cgi/en/se...d&sum_target=7

Access map:
http://www.tokyustay.co.jp/e/matrix/...Stationmap.jpg

On a mostly off topic note - New Chitose airport now has a Manyo club onsen in the airport
http://www.tenkai-japan.com/2012/01/...t-in-hokkaido/