I’m sorry but I don’t know the “best” bus line along the coast. I do know that some bus lines tend to travel the coastal road and some cut across (for instance from Guayaquil to Manta.) So if you visit many of the coastal towns, you’ll probably want to first go from Guayaquil to Salinas and then hop buses from town to town, which should be easy enough and very inexpensive.
It depends on how far you are going up the coast. CLP is an excellent line that will get you as far as Olon. Reina Del Camino goes as far as Bahia, I think. Beyond that I don’t know.