TO GET STARTED...
I recommend IC cards and discount tickets. It will save so much of your time and $$. Don't be lazy, just get it.
Getting Around TokyO
Tokyo's public transport system is the envy of the world. Most used by locals and travelers is the train and subway system. You will hardly get lost with English signage everywhere.
Train and subway The fastest, cheapest, and most convenient way. Locals use apps to look up transit. Map apps like Tokyo Metro Subway (simplified and easy to see) and Rail Map Line (covers broad area and detailed) have transit features but it's hard to use. Google Map is the best for English app so far. Locals use NAVITIME or Norikae Jourdan (try if you can read Japanese)
Taxi You can catch it anywhere anytime unless there is an typhoon or snow. It's quite pricy so good for a group tour. The only option to get back to your hotel after the last train. Don't rely on Uber, no one use it here.
Bus It could be a bit complicated. It runs thru small side streets, so locals who live far from the station. But there are many tour buses which can take you to tourist spots.
Walking some stations are very close like 5-10mins away. I always walk from Harajuku to Shibuya station! It feels great and save $$ at the same time.
Bicycle There are many hills in Shibuya, Shinjuku, and Roppongi, but it is a fun way to get around. Rentals are available. Some hostels lend it.
Rental Car tTo be honest, you don't need it unless you are going out of Tokyo. I usually rent it to go to IKEA and COSTCO once in a while but that's it.
Getting out from Tokyo
It's the cheapest way to get out of Tokyo. Ride could be really long but usually highway buses are comfortable and have toilets. Remember to purchase tickets in advance. many ski spots and hot spring areas doesn't let you get there by bullet train.
Not only in Japan but in Asia in general, there are many LCC airlines. Especially Vanilla Air, Air Asia, Peach Aviation, and Jetstar often have sale for domestic flights in Japan. Try to book early for the better deal!
It's pretty expensive. Sometimes, taking a air way ends up cheaper. Get JR PASS. That's the solution. Round trip form Tokyo to Osaka is almost the cheapest ticket fare.