It is interesting that for all its culinary marvels, Tokyo has so few good breakfast options outside of hotels. If talking about stand-alone restaurants, I struggle to think of anything that's better than, say, Bills. Which is perfectly tasty but it's a place where mama-tomo take their babies out.
I was momentarily excited when I saw that Sarabeth's had come over a few years ago, but they dumbed it down a LOT for the Japan market, apparently figuring that only bored housewives would go out for breakfast.