I liked the Tokyo Hilton.

Get on a Nirita express train to shinjuku they go ever half hour I think. Ask at the JR desk as some Nirita express trains go to Tokyo Central and stop, while some then go to Shinjuku. The Shunjuku station is about a 1/4 of a mile from the Hotel. The Hilton has a free shuttle that can pick you up, or there is a some what underground walk way that gets you almost there.

Enjoy!