Tokyo is an extraordinary city, with uncountable number of things to do and see. I strongly recommend going to the new Skytree Tower (the over 600 meter high radio tower).
Insider Tip:Even if you have the Japan Rail Pass, you will probably have to end up buying the one day pass for the subway, as the transportation system in Tokyo is so big that it takes quite a while on foot from the JR station to the sites of interest.
If you plan to visit the Tsukiji Fish Market and watch the auction, you´d better be there at 3 am in the morning !! Otherwise you won´t be able to enter as there is a very limited amount of tourist that are allowed in.