Solved. For notification icons which are different from the main launcher icon, create a folder called 'notification-icon' in your resources/android folder and upload your zipped icons there. One icon for each supported density and each icon in it's respectively named drawable folder (e.g. drawable-mdpi).
Then add this to your config.xml between the android tags:
code<resource-file src="resources/android/notification-icon/drawable-mdpi/notification_icon.png" target="app/src/main/notification-icon/drawable-mdpi/notification_icon.png" />
<resource-file src="resources/android/notification-icon/drawable-hdpi/notification_icon.png" target="app/src/main/notification-icon/drawable-hdpi/notification_icon.png" />
<resource-file src="resources/android/notification-icon/drawable-xhdpi/notification_icon.png" target="app/src/main/notification-icon/drawable-xhdpi/notification_icon.png" />
<resource-file src="resources/android/notification-icon/drawable-xxhdpi/notification_icon.png" target="app/src/main/notification-icon/drawable-xxhdpi/notification_icon.png" />
<resource-file src="resources/android/notification-icon/drawable-xxxhdpi/notification_icon.png" target="app/src/main/notification-icon/drawable-xxxhdpi/notification_icon.png" /> /code
Finally, edit your home.js file in WEB_RESOURCES/app, adding a comma immediately after the senderID and then on a new line add this:
codeicon: 'notification_icon'/code
This is outlined on the pushplugin page here.