These are some sweet sleeping coffins found only at Haneda!
Rule #1 of Okinawa travel, if you want some good mainland access try Haneda airport and not rely only on Narita, also don’t assume that JetStar, Peach or Vanilla are worth the “savings” especially if you want to check luggage. Haneda is a huge airport that is much closer to Tokyo, and has many more flights per day to Okinawa. Narita on the other hand is over an hour away via train or bus pending traffic:
To get to Tokyo from Naha the cheap and easy way you can use Experience Japan on ANA and earn United Miles or Japan Explorer on JAL and earn American Airline Miles. Both are only 10,800 yen or $96 as of today.
From the states there are 2 direct flights from SFO to HND: United 875/876 and JAL 1/2 which you can use miles to book. For United it will cost $1,157 RT or 70,000 + $35.86 and for JAL you can book on American Airlines as AA 8400/8401 for $1,157.66 but could not find any award space for it.
So book that international segment first, then use the ticket number to book the domestic flight on Experience Japan or Japan Explorer for $96 a segment this is the same price as Peach but a lot better times and service, also includes luggage. There are more options to mainland other than Narita on Vanilla or Jetstar where they have no complementary refreshments in flight, (not even free water (they ask you to drink the bathroom water)). There is a single flight on ANA to and from NRT ANA 2158/2159 but if you miss it you have to wait till the next day. This has happened to me once. Below are the flights on ANA and JAL to and from HND to OKA as of today. Ignore the prices, because its only $96 per segment using these gajn programs.
From OKA to HND:
And going from HND to OKA:
P.S. Thank you Nathan for the edits