Upon arrival in Tokyo Narita International airport (or just before you leave!), don't just rush headlong into the city... If you have come long-haul and are tired, there's nothing better than to get your head down at one of the airport hotels for a few hours, and then use Narita as a gentle introduction to Japan/Tokyo. It is a nice small town, which is very walkable, and has many little gems including a temple, local restaurants, shops and backstreet pubs. Prices for food, hotels et al will be much cheaper that Tokyo city, and it allows you to acclimatise in a much less hectic/congested atmosphere. I have always found it a perfect way to take a breather before business in Japan and/or exploring the country on vacation.

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You should cultivate friends in locations where you are planning to visit. Make contacts on internet bulletin boards and seek advice from like-minded locals on any activities/hotels/restaurants etc.

This is always the best way to minimise your risk when visiting a new city (or even one that you have been to many times!). Also, be prepared to help others with advice on your own city also :-)

www.flyertalk.com
www.lonelyplanet.com
www.tripadvisor.com

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Why not try hotels down near Battery Park or in the Financial District and commute by subway/taxi to Midtown? Typically hotels can be half the price outside Times Square and environs, and often 'try harder' to impress guests. Also, the Hyatt just across the Hudson is another great option - right next to the PATH train and also has a water-taxi service to Manhattan close by. Again, it is often less than half the price of equivalent city hotels, and has a stunning view of the city as your night-time panorama!

www.hyatt.com
www.hilton.com

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