It all depends on where you go. Komeda coffee shop have a morning service that includes a boiled egg, a buttered piece of toast and a coffee for around 350yen. Mr Donuts has okawari American coffee, that means they will keep refilling your cup, my best effort was 4 refills, not bad at around 300yen. Starbucks was around 330 yen for a tall Sumatran coffee recently. And of course vending machine coffee is around 120yen per can. These prices may vary a little but they are pretty much what you would expect pay all over Japan.