My heir is unfit for the throne. How can I make him aware of this fact?

There are no direct covert actions that will let you kill your heir. However, do not lose hope, for there is still a chance at murder.

• There are a few random events that can either: a) let you choose an option that kills your heir or, b) simply kills your heir (the hunting accident event, for example)

A much more direct approach:

• You can assign your heir to become a general in the Military tab. Then, put him in command of a thousand brave troops and send him to war against an overwhelming enemy. Repeat until he is dead.

With the Rights of Man DLC enabled:

• A country may disinherit an heir if so is wished, at a cost of 50 prestige. After this action is done the country won't have any legal heir and will be at risk of falling under a Personal Union, just like any other country without a legal heir (It is not possible to "return" to the disinherited heir).

If you don't mind using cheats, there's a console command: kill_heir