Current exchange rate as of 2017-01is ¥120 : $1, lower than the historical ¥100 : $1 - so stuff is pretty cheap right now. Still, despite common US assumptions, JP is pretty affordable in general. Food, hotel, transit are all comparatively cheaper than LA/SF/NY prices. Certain hard goods like JP cameras, headphones (some more notes) and Apple computers might also be significantly cheaper.
Get a Suica card immediately (can buy from machine for ¥2000 (¥500 refundable deposit for the card, ¥1500 initial balance). This will make your transportation life much easier - otherwise you have to buy separate tickets for each subway line and it's confusing/terrible
The Suica card can pay for subways and sometimes buses across Japan now. All IC cards are basically interoperable across the country although some buses are still cash only. You can recharge your card at any JR terminal/service desk (or most konbinis). You can cash out your balance when you leave (or use it w/ vending machines or konbinis so there's no reason not to always have it charged up)
There's 7/11 or Citibank ATMs when you arrive in NRT. Go there first.
The Skyliner is a super fast way to get to Tokyo Station from NRT. You may want to consider the Narita Express if you need to get to the west side (Shinjuku, Shibuya) and don't want to transfer, but the Skyliner to Yamanote will probably be faster/cheaper anyway (if you have a long wait or need to use the regular/local Sky Express train, then maybe consider the NEX)
You pay maybe a $10 premium, but if you want data as soon as you land and don't want to go searching for a SIM at BIC or Yodabashi, it's totally worth it and I'd recommend buying at the airport for most people.
IIJ Travel SIM of Freetel Travel SIM
I've used this the past few times. It's convenient, does the job. You can install a profile that gives you the APN settings (disable/remove when done) but there's no registration involved
Freetel is nice since you get free FB/WeChat/LINE data (not counted against the cap)
For Tokyo, first timers tend to book the fancy hotels in Shinjuku - do yourself a favor and don't do that. 1) Shinjuku station is the worst (huge, confusing as hell, far away) and those hotels are a further 10-15m walk from the station, out in the middle of nowhere. You should prioritize convenience to subways (particularly the Yamanote line, which is JR and takes you in a ring around the city). Shibuya is super hopping, but may be a bit much. Personally, I like Ebisu as a great neighborhood, that's walkable to Daikanyama, Yoyogi, and on the Hibiya and Yamanote Lines. You can of course go w/ somewhere on the east side as well. I've had great experiences w/ AirBnB but the city has been cracking down on rentals, definitely make sure you contact the host and make sure you're sorted, especially if its your first time in town.