Can I display top charts in my app using album artwork from iTunes?
It seems to me that what Apple's email says is going to be the most important thing here. 

For example are they asking you to remove the artwork? Or are they just trying to inform you that they're getting complaints?

My thinking would be that since you're publishing an app on Apple's App Store that you'd have to take their email as a strong indicator of what you can do (or need to do).

As a registered Developer, you can also call Apple Developer Program Support in your country for clarification/guidance.

Finally, if Apple wants you to stop showing the artwork, it may be worth mentioning the other apps to them. However, it is entirely possible that Apple has also written to their developers too asking them to take the same action.