There are literally too many guides are Tokyo, so here are just my favorite three things in the east capital.
tsukiji fish market
Whatever anyone tells you, the tuna auction is literally SO. MUCH.FUN. What is not fun is getting up to wait for the tickets-- they give the tickets away from 3-4 am so I recommend you line up around 2:30 at Kachidoki Gate. The first group of visitors are admitted to the auction between 5:25 and 5:50, while a second group of 60 visitors are admitted between 5:50 and 6:15. There are number of 24 hours sushi places
The wait for sushi dai (click the link for how to get there-- it's confusing) was 6 hours the last time I was there, and honestly, my palate is not refined enough to appreciate the difference. My choice is right around the corner-- see the photo below for name. My favorite sushi chef is the one at the very back, who has worked for over 25 years as chef. He has a great sense of humor, and because he lived in Germany and New York, his English is pretty good. The sakura plate is my favorite.
The entire market is scheduled to move in November 2016, which makes me very sad :(
Obviously there is good food everywhere in tokyo, but Ebisu Yokocho is an adorable food alley with a twenty something different taverns that all serve different things from cow tongue to horse mackerel. It has a very local crowd, and starts filling up quickly around 7ish so go early-ish to have a better pick. Since they're all different, it's best to barhop!
shopping in harajuku
Yes, I know cliche but it's just so GODDAMN CUTE. Kawaii Monster Cafe may be my favorite place in the world, but it may give you nightmares as well. Other people have so many recommendations for specific stores, but turnover is so high that the best thing to do is wander aimlessly and browse through! You're gonna find some weird gems.