Re-bonjour
Empress,
The Narita Hilton just became a Hilton, explaining the dearth of posts:
http://www.flyertalk.com/forum/Forum57/HTML/003934.html
I would pick the Narita Hilton for convenience, and the Tokyo Bay Hilton for relaxation.
The Shinjuku Hilton will be worth the extra Y10,000 only if your flight leaves later in the day. Tokyo closes down at midnight for all practical purposes, and a morning flight entails leaving Shinjuku after an early breakfast (about 90 min./U$35 by Narita Express, from the faraway 'New South Exit').