I see both on Google Books.
Which is the correct option?
Example sentence:
Mary and I picked a table at/in the back of the restaurant.
Did you eat at the restaurant or in the restaurant? Both are correct, the difference is whether you picture yourself at a location or inside a building.
In the same way, do you see yourselves at the back of a location, or inside the building, near the back? Both are fine.
You can also say "by the back", "toward the back", "near the back", and various others. Each has slightly different nuance.
The restrooms are down that aisle, toward the back of the store.
The restrooms are by/near the back of the store, next to the loading dock.
There can be a distinct difference in the two. Here's how I would interpret each:
We ate the back of the restaurant.
Expresses you chose a table on the regular dining floor at the opposite end of the room from the door.
We ate in the back of the restaurant.
Expresses you ate probably in a separate room located behind the regular dining floor. 'In' suggesting you were in a different enclosed space. You would also direct a delivery person to put an item 'in the back', presumable where the storeroom is located.