The biggest rivalry over US-Haneda dominance is between Delta and American, who are also offering a double miles promotion on their JFK to Haneda route, a direct flight which is supposedly on special, costing a TOTAL of $858. We say supposedly because we've been searchingand not findingthat sale airfare. The cheapest we can find for that exact route is instead $947 total.
Conclusion for NYC to Haneda routes: It really depends on who you're more loyal to...American or Delta? American's flight is direct from JFK (our preferred airport over Newark), but costs almost $100 more. Delta's leaves from Newark, has a quick connection in Detroit, but costs almost $100 less. Both offer at least double miles as a bonus.
For you west-coasters looking to hit Japan for the cherry blossoms, your choices aren't much cheaper than flying out of New York. The best price is $817 total for a direct Delta flight from Los Angeles. That'll get you the double miles bonus too, remember. Following that is $818 total for a direct Japan Airlines flight from San Francisco. Or class it for almost $100 each extra from LAX and SFO and go for a route that includes ANA.
So many choices! So much savings. Tokyo in spring FTW. Obviously if you spy any rates than these we found, do let us know in the comments below!