The easiest way is to edit the file adthosts.py from the AutoDockTools folder and replace autogrid3/autodock3.

#AutoDockTools/adthosts.py
hostMacros = {
    'localhost': { 'host' : 'localhost',
		   'autogrid' : 'autogrid3', # replace autogrid3 with autogrid4 path
                   'autodock' : 'autodock3', # replace autodock3 with autodock4 path
                   'queuetype' : 'int',
                   'userSpecific' : 0 },
    }

The problem with this approach is that when you update ADT using Help->Update menu, you need to redo this for the updated adthosts.py as well. The other way to make ADT remember the path is to create a file called _adtrc in the current working directory and paste the following code in there:

import socket
localhost = socket.gethostbyname_ex(socket.gethostname())[0] 
self.ADstart_editHostMacros.addItem_cb(macro=localhost, host=localhost,autogrid='autogrid4',autodock='autodock4',queuetype='int',userSpecific=0)

Since ADT runs _adtrc when it starts up, this approach should survive across updates.