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Areas

Shinjuku Station

Shinjuku station is infamous, but as long as you're going between train lines, just follow the signage - it's pretty developed at this point. Note that odakyu lines are in a separate area, separated by the odakyu mall.

If you're trying to get to a store inside of Shinjuku station, then good luck.

Skytree

One of the main observation decks. It's a bit of a tourist trap, but it's not that bad. Some people consider the view the worst, since it's more out of the way, but if it's clear you can see Fuji, which is nice.

Mount Takao

Very popular daytrip from Tokyo, so best to do it on a weekday if possible. On a clear view, you can have a nice view of Tokyo again

Teamlabs

Semi-phase art exhibit/museum/kinetic art show. Buy your tickets at least a few days in advance. Borderless is more about a light show, and Planets involve, uh, "water". Don't wear a skirt to either. For Planets, wear shorts or pants that can be rolled up.

Restaurants

Hinoya Akihabara

For some reason, this particular branch just tastes great. Probably the only food in Akihabara I'd willingly eat.

Yakitori Tsukada Shibuya

Google Maps
Address: Japan, 〒150-0043 Tokyo, Shibuya, Dogenzaka, 1 Chome−6−8 楠本第２ビル 2階

Some of the best food I've had in Japan. You need a reservation, but a few days in advance is usually fine. Get the reservation on tablelog.

Glitch Ginza

Internet famous coffee places. Speaks English, makes a pourover with beans of your choice. Expensive, but it's a good experience.

Sushi Zanmai

Probably the best of the cheap sushi chains. The main store is 24/7, so an option for very late night sushi adventures.

Stores

Japan Blue Jeans

In Shibuya, sells Japanese selvedge denim of good quality for good prices (~$200 each). Has English speakers

Zabou

Has a store in Ginza and Shibuya, which have different stock. Has somewhat niche Japanese brands which are a blend of streetwear and Americana.

Map Camera

Used camera store in Shinjuku. Has an online catelogue and speaks English