Here is the list of the most reputable Japanese travel booking websites. They are operated by the largest and oldest Japanese travel agencies, JTB, Kintetu and Hankyu.
The difference from the multinational booking services such as Trip Advisor is that they have their own unique products that they have developed over several decades of their operations in Japan. And the level of the services you can expect from them is exceptionally superb. That is Japanese quality.
As you can notice by browsing their website, there are varieties of packaged tour products as well as one-off short optional tours. Many of them are attended by an English-speaking tour guide.
Their websites are good sources of tourist information about Japan as well. There are information blogs about tourist destinations and activities and many neat photographs of them. This is because they have incredible amount of data accumulated over the long-lasting operations. Remember, they are the oldest and biggest players in the Japanese travel industry.
If you want a real Japanese experience, check them out.
JapaniCan by JTB
Japan Traveler Online by Kintetsu
Travel to Japan by Hankyu