There are always direct flights to Tokyo available.
Transportation is very convenient in Tokyo. Depending on where your hotel is, taking the regular subway can cost you JPY120/~USD1.10 upwards. If you like the convenience and plan to come back to Japan, I suggest getting a Pasmo card. It costs JPY500/~USD4.59 for a personalised card but you can load it up with at least JPY2000/~USD18.37 to last most of your trip. You could also use the Pasmo card to pay at vending machines and convenience stores like 7/11 and Family Mart. Another card you could get is the Suica card. You could reload these cards at any train station.