You need to be extremely careful. SharePoint does not delete lists by default because it does not want to destroy customer's data. If the customer has added data to the list or "re-purposed" it then they will be very angry when you destroy their data.
When you say "External List Instances" I assume you mean BCS External Lists. If so then your list will not contain any additional data but the list instance might have been customized by the user (View or Query).
If you are you really sure you need to destroy the list and any customizations it contains then I would suggest an SPFeatureReceiver and on FeatureDeactivating use the object model to find the list and delete it.