Filipino boxers have had a good showing from the year 2000. No doubt many would pick Manny Pacquiao as number one because of the several weight divisions he is champion. On a personal choice, I pick Nonito Donaire for the top Filipino boxer followed by Brian Viloria and third, Manny Pacquiao.
Why? Nonito Donaire has successfully defended his title and very convincingly won over his opponents. Most, I believe, did not go the distance. Brian Viloria lost his one or two earlier 2000 fights but did a very convincing comeback defeating almost all, if not all, that were favored against him.
Manny Pacquiao holds several titles but his recent fights from 2011 to the present were not convincing, even if he won some of them. The big difference comparing Donaire and Viloria to Pacquiao is, he (Pacquiao) is too "politicized" and "religionized". Political and religious people were too quick to pounce on Manny Pacquiao for the money he was making, knocking him out of his focus in boxing.
What politics and religion did to Manny Pacquiao is not crab mentality but actual crab actions pulling down Manny from his achievements. They made him believe that politics and religion did him well in boxing.