Option A, seating first offers more window space/natural light to the customer; however if there is a long line/queue then the congestion could spill out into the seating area, making the seated customers uncomfortable--but also creating a higher seat turnover rate.

Option B, coffee bar first encourages the line/queue outdoors, providing free advertising for the coffee shop: i.e. "this coffee is good", but moves the customers away from the natural light and more comfortable dine-in experience.

In the end, I think it depends on the location of the shop. Is there another coffee shop in the area? If so, maybe offer the opposite layout that they offer. If it's mostly a rush-hour/lunch urban clientele, then maybe Option B up-front is good. But if it's a bad weather type town, then maybe Option A is better so more customers can queue up under shelter. 

Personally I prefer Option A though. More time to peruse the menu and people-watch as you make your way to the order station.