Having visited Tokyo in May and New York in December I can say that Tokyo is a relative bargain, and this was true even before the yen's recent slide. Top hotel rooms are cheaper, and you can get a decent restaurant meal at all price points for much less in Tokyo. Lunch $10-15 (v. $20 for a fatty deli sandwich), Sushi dinner (not the boats!) for $60. And for $150pp you get a tremendous Michelin rated sushi experience in Tokyo. In NYC you get an overpriced meal at a "name" restaurant that will still leave you hungry and you tip on top of that for sometimes marginal service. Museums are $25 entry in NYC - I don't believe we paid more than $10 in Japan and usually less.
I told Mrs. B I would gladly take her back to Tokyo anytime, but NYC maybe once a decade as I now view it as a huge tourist rip-off. On the plus side, it makes overpriced SF look better.