For Tokyo, I cannot recommend the Conrad enough. It's new, beautiful, elegant, and spacious. It's right next to the rail station and two department stores. It's also within walking distance to the Tsukiji fish market and Ginza. Besides, you'll get the bear and the duckiES!

I haven't stayed at the Hilton Tokyo but it's in a good busy area (Shinjuku) if you'd like to stay late out at night, you won't have to hurry to catch the train which stops service around midnight.