If you'd no longer like an app to be available for download in the iTunes App Store, you can remove it from sale right through your iTunes Connect account. Just follow the steps below to do so.
Note: If you wish to prevent current users from accessing an app's content by deactivating it fully, follow the instructions here.
1. Log into your iTunes Connect account.
2. Click the My Apps section.
3. Select the app you'd like to remove.
4. Click the Pricing and Availability tab on the far left.
5. Under Availability, check the box for Remove from sale, then click the Save button at the top right.
6. Return to the My Apps section by clicking the navigation button at the top left.
7. Locate your app once more, and you'll see the status has changed to Developer Removed From Sale.
8. Within 24 hours (though usually less) your app will no longer appear in the App Store.
Additional Article from Apple:
Apple - Remove an app from the App Store