The El Nido lagoons are some of the nicest scenery in the Philippines, if not the world. But having been discovered long enough ago, they have become inundated with the usual swarms of tourists bobbing in their obnoxious coloured life preservers.
You can check out the discussion on tripadvisor for various suggestions on which tours or companies to take. Generally, the Art Cafe seems a safe bet, but the good word on the street is that many of the operators go in the same direction, such that the travelers on many of the different boat companies end up following each other in a big wave.
If you would like a slightly different approach, a friend of our friend likes to go in the opposite direction, so you have a better chance of enjoying an entire lagoon for your small crew alone:
Or just rent a kayak, as explained on the El Nido page, and check out the lovely shoreline nearby. Otherwise, if you are limited for time, you may be better off checking out the lagoons in Coron, much less invaded than El Nido, and more worthwhile as suggested in this tripadvisor thread.
Enjoy your bobbing!