Okay, you've got your smartphone and your pocket wifi. Time to have a wander.
Getting from the airport to the city:
I've always flown into Narita, so all of this is specific to Narita. I don't know anything about Haneda. You can take a bus into the city for about $25, but it will take about two hours (plus another hour to get from the dropoff to your hotel). I always take the Keisei Skyliner. It's about $45 one-way, but the seats are super-comfortable, the ride is smooth and quiet, the view is nice, it takes only 40 minutes, and in every seat there are outlets for recharging your phone. For me, it's worth the extra expense.
Some notes regarding the train:
- When you get your Skyliner ticket, the clerk may say something like, "please hurry." They mean it. Every single time I buy a ticket, the train is set to depart in about two minutes. There are nice clean bathrooms on the train, so don't worry.
- All seats are assigned. Just get on the train right away so you don't miss it, then find your seat.
- Near the doors, there are luggage racks for your big suitcases.
- Nobody is going to steal your stuff. You could leave your phone and wallet on your seat and disappear for 15 minutes. They'll both be there when you get back.
- Train announcements will be made in Japanese and English.
Once you're in the city:
In all subway and train stations, you'll see machines for purchasing a rechargeable card for using buses and trains. There are two: SUICA and PASMO. Pick one. They'll both work on all Tokyo trains and buses, so I guess you can pick the character you find the cutest. If you have time, get one at the airport before you head in to the city.
I always load mine with ¥10,000 (about $100 USD). I'll spend about ¥500 / $5 a day on the train, so it makes sense. Don't try to buy individual tickets for rides. It'll take forever and you won't save any money.
Using the trains and subways:
There are, I think, six or seven different private companies running trains and subways in Tokyo. You'll find paper maps everywhere, but some of the maps show some lines and not others. I use an iPhone app called MyTokyoNavi. It's very simple and will give the simplest routes. However, you may want to use more than one app to double-check.
The JR Yamanote line is going to be your best friend and worst enemy. You may end up using it a lot because it runs in a big loop through central Tokyo, but of course a billion other people are going to want to use it, too. If you can, avoid trains during morning and evening rush hours. That is, unless you enjoy being compressed.
If you ride the Yamanote line late after 10pm on Fridays or Saturdays, expect to see some drunk locals puking. It's normal here, and somewhat acceptable. Just watch where you walk, if you catch my drift.
Finally, Tokyo's trains do not run all night long. They will have their final runs around midnight, so if you're planning on doing some late-night drinking, try to do it close to where you're staying unless you want to keep drinking until 5am when the trains start running again.
Questions? Feel free to contact me directly: firstname.lastname@example.org