I would recommend avoiding the wet season (southwest monson) which is during May to October. Locals call this monsoon "Habagat". It is more rainy during this period and you may get really unlucky and have your trip coincide with a typhoon (we get several a year, bringing heavy rains, winds and flooding). Even during this period, you can still get prolonged sunny periods and nice water conditions... roll the dice.
The 'dry' season is from November until May. This is the northeast monsoon, called "Amihan" locally.November and December are typically the cooler months. Water temperatures can drop in some locations, requiring 3-5mm wetsuit. Most people here just enjoy the cooler, less humid weather though. Temperatures rise in the new year, peaking during April-May, when max temps are around 35C.
It can also be worth avoiding the primary Christian holidays of Christmas and Easter, as a large percentage of the population will travel to visit relatives etc at these times... so getting internal transport (bus, plane, ferry) can be very difficult.