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This has been asked many times, do a search. In short, Anilao, Subic or Puerto Galera. All have their pros & cons
Anilao/Batangas - 2 hours from southern edge of Metro Manila. Primarily famous for muck/macro/photography. Expensive resorts, but some offer unlimited shore diving.
Puerto Galera - 2 hours from southern edge of Metro Manila, plus ferry. Variety of diving, with some pelagics. Cheaper accommodation.
Subic Bay - 3 hours from northern edge of Metro Manila. Historical Shipwrecks, wrecks and more wrecks. Wide variety of accommodation and nightlife.
Transit time around Metro Manila can vary enormously depending upon (1) the weather, (2) the time of day, (3) the day of the week and (4) public holidays etc. On the worse days, it can take as long just to negotiate the Metro Manila traffic as it does to complete the rest of your journey. If there are heavy rains/floods, then Metro Manila can grind to a literal stand-still for many hours.
Some links:
General Philippines Travel Advice: Philippines Travel Advice | Scuba Diving | Holiday Information
Subic Bay Dive Sites and Wrecks: Subic Bay Dive Sites | Map and Descriptions
Subic Bay Marine Life Photography: Subic Bay Underwater Gallery | Marine Life Photos
Travel Directions to Subic Bay: Travel Subic Bay | Directions for Travel
Anilao/Batangas Dive Sites: Scuba Diving Anilao and Batangas, Philippines | Dive Sites