There are quite a number of cruise ship and water taxi companies working on Tokyo Harbour. Many of them specialize in serving meals on board -- very often after dark so that the patrons may enjoy the city lights around the harbour. 

As can be seen in the photos we took there are a great variety of types of craft. 

There was no meal offered on the cruise we took in the late afternoon - but it provided a fascinating view of the many types of buildings and activities visible while we travelled around the harbour.