Going to Japan for my honeymoon sometime in the fall of 2014 and Tokyo is one of the stops. Does anyone have any favorite hotels there? Since this is for my honeymoon, we don't mind splurging and actually prefer to stay somewhere nicer!
I just spent my honeymoon in Tokyo last month and enthusiastically endorse the Park Hyatt Tokyo (which you may recognize as the hotel from Lost in Translation) as a splurge hotel. Fair warning: Shinjuku is not the most central location, and if that's of paramount importance this probably isn't the spot for you. That said, what it lacks in convenience it more than makes up for in service, amenities, and truly the most magical hotel bar anywhere in the world. If you do stay, make sure you take advantage of their free shuttle to and from Shinjuku station for getting around by train.
Here are my favorite places to stay in Tokyo:
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Check out The Ritz-Carlton, Tokyo. The lobby is breathtaking and the concierge went above and beyond to help us and make sure we had an amazing trip and easy time getting around. Also, afternoon tea is really fabulous.
This is not exactly in Tokyo but since you mentioned that you're happy to splurge I recommend looking into
I haven't been myself but wanted to go badly on our last trip ever since I read up about this place in a couple of travel magazines and blogs. Depending on when you are going they sometime have special rates up on their website.
Definitely check out the various rooms, hot springs and spa offerings. I believe there's a shopping area nearby the train station too.