Tokyo is easy to get around and the trains/subways are fantastic. We've taken NEX from Narita to Tokyo then transferred to the Keiyo Line out to TDR. Some folks don't like the transfer, but I enjoy the walk and experience of the Tokyo Station. If not, check out buses as taxi's are expensive.
If you stay at an official TDR Hotel and they offer park tickets, buy the regular two day (park specific) then day 3/4 as hoppers. DON'T buy Hoppers for all 4 days. You'll have enough to see and do in each park the first time you visit. We bought them and never used them.
Use a good general hotel booking website to compare prices with locations around TDR or Tokyo. Use the subway system to your advantage if not on site. The Disney Celebration Hotels are about a 15-20 minute bus ride from TDR or 5-10 taxi ride to Shin-Urayasu, then 5 minute subway ride. Typical Japanese mid-range hotel room with split bathroom. I'd stay away from the bunks if the boys are above average size. The hotel is very nice; however, there are limited services (restaurants and stores within short walking distance) in the area. We used taxi's and the local bus a few times to shop and eat.
Use ATM's at the airport, hotels, Ikspiari (downtown disney) and convenience stores (7-11, Lawson's & Family Mart) for cash.
Use both the TDR Explorer and DisneyTouristBlog sites along with TDR. They're a great resource.
Enjoy!