The Tsukiji Fish market, located in central Tokyo, is one of the largest and busiest in the world. For the early birds or the jet lagged, this is a perfect place to visit when in Tokyo. The live tuna auctions starts at 5am, it’s amazing to watch. You do have to check if that day there is access, as sometimes it's too hectic for them to have tourists around.
If you plan to go later in the morning, the other shops in the outer market open at 9am. But a visit to the market is never complete without having a fresh fish breakfast in one of the local counter-restaurants. People start lining up early in the morning for a nice sushi breakfast of the day’s catch. In the outer market you can also find other things like ceramics, Japanese knifes, and other utensils.