At any given time, Koffee Mameya has 15 to 20 different beans on rotation from indie roasters around Japan (and some from overseas). Get a cup brewed on the spot or purchase beans for home use; English-speaking baristas can help you narrow down the selection. There's no seating, but you can loiter at the counter.
It's a little tricky to find; look for a beige building with an alcove and a stone path.