Places I've been to and can recommend.
Some are better for a cozy afternoon with a book (e.g. Bonanza Roastery or The Barn Roastery), others are better for a filter coffee to go (e.g. Concierge).
Coffee Roaster · Kollwitzkiez · 286 tips and reviews
Timo H: Perfect on a Sunday morning, not crowded, really chill. Appreciate their no strollers & laptops policy. Can add nothing about the coffee, which of course is amazing.
David Noël: Excellent coffee shop close to Checkpoint Charlie. They carry Five Elephant coffee, have a nice selection of magazines and provide space for working. More Soho than Mission. Great spot.