I've never stayed at the Hilton Tokyo Bay, but it may be a little far to commute to downtown. The Hilton downtown (Shinjuku) is nice - I've stayed there maybe 7 times in the last year. The Executive lounge offers breakfast, appetizers and cocktail hour, although the food leaves a little to be desired. I usually don't have any problems upgrading to Exec with a coupon, but they can be rather full at times. Indoor pool and fitness center (email me if you want to make sure you have a fitness center free pass - $$ if you don't.)

(Sometime on my way back to Narita I would like to try out Hilton Tokyo Bay.)