Terminal 3 has a "left luggage area"
look for it on the ground floor, open 6am to midnight http://www.filipinotravel.com.ph/information/faqs.php#6

Not sure if there are any other
lockers but an alternative is to have someone outside the airport store them. http://www.friendlysguesthouse.com/ offers this service you could also get a taxi around town and have the driver keep them while you sight
see. If you go to Mall of Asia they have a baggage storage there.