There is nothing inherently evil about an app, or inherently good about a website - it's only because historically we have allowed crappy app permissions structures and allowing apps to ask for things they don't need.
Apps are faster, are more predictable (no auto-reloading or rendering issues) and generally perform better IMO.
On the other hand, in reality, you're correct. I think the NYTimes app will collect more data from me than the NYTimes website.