Go early in your trip, like the first or second day - you'll be jet-lagged and up early anyway. The tuna auction happens really early, like 5:30-6am or something like that, then wander outside to the sushi restaurants for some of the best sushi you'll have in your life.
This is an awesome thing to do, if you love fish. You will need to wake up early and get the very first train of the day and you have to transfer off of the JR lines to a private line. I can get you the details if you need them. You get up close and personal with large Tuna and all kinds of exotic seafood. The auctions are a sight to behold.
do this trip as soon as you get to Tokyo, so that it's easy to wake up early while you're still adjusting to the timezone. best to get there by 6am (check times for subway). entrance can be a little hard to find, but once you're inside it's a bustle of activity.
I could people watch all morning at Tsukiji, world's largest fish market. The diversity of offerings can delight any seafood lover's cravings. Go early to watch the auctions. You won't believe the prices some of these fish garner.