I do not remember very many great cruises around the Philippines, but I know some cruise lines stop briefly, but you can jump onboard a ship almost anytime. We visited the Philippines a few years ago to visit a friend that lives there. We rode a ferry from Manila down to Dumaguete and were aboard the ship for about 24 hours.
You would not classify it as a cruise. No luxury was involved. Meals were very basic. The only entertainment was the television and the water. We saw many day cruises on small vessels, but not many offers for longer cruises. There is one cruise we have looked at a few times that goes from Hong Kong to Manila and takes about 3 days, but I do not remember the cruise line now.