Landing in Tokyo is very practical, and indeed this is often your first city in the itinerary in Japan. However, this is a HUGE city, and moving around the different neighborhoods and centers may look scary if you don’t have enough confidence with the transportation system.
So let’s talk transportations in Tokyo.
Transportation in Tokyo
Once you survive the first traumatic impact of people flooding in the subways and in the trains, I promise that moving around with the public services is very comfortable – and easy, actually!
First of all, I suggest you avoid buses: sure, they are fun, and as usual efficient and on time. However, they are small and often uncomfortable for taller people; moreover, they may suffer little delays for the traffic.
I strongly recommend you use trains and metro: generally speaking, if you have a JRPASS, you will be able to move around the city using only the JR lines – thus not having to pay extra money. The most popular is the Yamanote line, who surrounds the city in a big circle; you can also find the Chuo line, very useful if you move from east to west, for example.
Then, of course you can use all the 9 different metro line: you just have to remember to buy the ticket to enter.
Finally, you have various private railways – such as the Seibu Ikebukuro line, for example – the will bring you to the suburbs of the metropolis.
And of course, you can always decide to move by feet: sure, you will have to spend 3 or 4 hours to move from one neighborhood to the other, but as I mention somewhere before, it totally worths the effort!