It depends on your purpose. Nylon is lightweight and stretchable yet still has a better strength-to-weight ratio. A nylon backpack is light but can endure heavy loads without breaking easily. But, polyester has got an edge over tear- and water-resistance thanks to its rough texture and extra-tight weaving patterns.
Given how technology moves today, plus DWR coating, whether a nylon or polyester backpack is better is no longer a question. Materials are not the primary factor when looking for a bag anymore, but their performance. And the best way to do that is by investing some time diving into in-depth reviews and customer feedback.