Japan is very different to their travel methods than we are used to here in America. Since Japan consists of small islands, its more efficient to take bullet trains or as the Japanese say, shinkansen. These high speed trains travel at almost 200 miles per hour and have an incredibly efficient standard, departing right on time to the second. The best part is everyone is at ease because there has been no reported history of any train accidents. The shinkansen network connects every large city or town in japan and is extremely cost efficient making it affordable to travel all over Japan at ease.

Source: http://www.japan-guide.com/e/e2018.html

Just like with most flights, the Japanese train offers three levels of ticketing exactly like coach, business class, and first class. Tickets are available for purchase online, at a train station or any train kiosk. Train tickets for any Japanese rail system are available anywhere tickets are offered. That include regular public transportation in Tokyo as well.

When it comes to Tokyo Metro, tickets range based on the distance to be traveled, however the most expensive ticket for Tokyo Metro can cost up to 3 Dollars.

Source: http://www.tokyometro.jp/en/
Expect it to be very jam packed in the train car because Tokyo has about two times as many riders as the MTA, but has fewer train lines than the MTA.