Nobu is supposed to be one of the best Japanese restaurants here, doubt you'd have picked it up from here.
But then again, if the food you picked at Family Mart in Tokyo was one of those sealed boxes, very doubtful you picked it up from there as I would assume they are extremely strict on their standards.
At the end of the day, pretty much all restaurants here will employ cheap labour who may not be as well trained as the head/ sous chefs, so you may actually have picked up the food poisoning at Nobu.