The really best place for obento I know is Asakusa Imahan at the Tokyo Station (inside ticket area, Gransta). There are several obento stores in the main passage, but you can‘t compare the quality with the one downstairs.
It‘s a whole area which only has shops specialized on different specialities of obento „manufacturing“. It‘s not experimental craft obento, it‘s just the highes standards of ingredients and preparation.
I‘ve chosen a beef yakiniku obento from a branch of the famous Asakusa Imahan store. It‘s just amazing, the taste and the composition.
Combined with some sweet covered potato stripes
Some other obento take away stores:
For those who want it fresh:
