I ended up taking a long walk in the old town and enjoying Café Schober and Babu's Bakery and Coffee. I recommend both.

Schober for a traditional hot chocolate in a historical setting, later in the morning, as we were making our way back to Hauptbahnhof. Great place to stop at and avoid the light drizzle of the morning rain for a while.

Babu's bakery and coffeehouse in Zürich is an amazing hipster third wave coffee shop, with lots of seating and a large selection of fresh viennoiserie, good coffee and a varied breakfast menu. I had the bircher muesli and a chocolatine with a latte. Nice big windows on Loewenstrasse, lots of plants, wooden tables, nicely decorated all around.

Enjoy Zurich!