I have noticed that stores in different areas have different quality of items for sale. Which areas have the stores with the best items? (I don't mean the best in the game, just the best available in stores.)

The Pit and Celeste sell the highest level items in their stores.

That's true. It wasn't until I first arrived to Celeste that I obtained the most powerful items. The stores there sell so much good stuff, and cycle their inventory too, that I could barely decide what to buy given my limited budget.