You could add it to the boil if you like, however you should have better luck getting the flavors out of them if you add them to the Secondary.
There are several washes that you can use, however I would peel them and add them to some water in a pot. Bring it up to 165F for 20 min. Cool and then add them to the secondary. This should kill any nasties and still retain the flavor.
Cheers
Preston