Every day of the week you can catch the tourist ferry between these two ports. The ride will supposedly average 8 hours and cost 2,200 Pesos.
From what I have heard the boat can take longer than the scheduled time and frequently runs out of food. There are many companies that offer this service but they all cost the same and from the services advertised no real difference is apparent. I personally did not go with this option. The hefty price tag of 2,200 Pesos it was out of my budget so instead my travel companions and I went for Option B, aka the Masochistic Local Boat.
Once a week, check departure schedule when in town, you can catch the local cargo boat between these two ports. The cost, including breakfast, is only 950 Pesos.
I took this boat from El Nido to Coron in Jan 2012. It was scheduled to leave at midnight but we were not allowed to board the boat till around 2am. This is a frequent occurence on this boat and the locals seemed to expect this.
Once we boarded the boat we were greeted with our first of many uncomfortable laughs. The beds we had booked on this "sleeper" ferry were nothing more than plywood bunk beds. I imagine prison beds to be similar. I fortunately passed out but my travel companions said we did not actually pull out of port till almost 4am.
Upon waking up due to rooster calls, I shared a few more uncomfortable giggles before setting off to find the bathroom. To my surprise they weren't as bad as expected. A head and bucket but clean enough, whew. After that was breakfast. This simply consisted of white rice, a hard-boiled egg and dried fish. I highly recommend stocking up on water and snacks for this ride.
The rest of the ride was spent reading and watching pristine beaches that dotted remote islands as we pass by. The tiny island in this remote region are breathtaking. Even to this jaded Island Girl. The other main on-board activity was touring the zoo. The zoo? You ask. Yes our boat was home to 1 pig, 2 chickens, 3 tanks of fish and clams and 50 buffalo.
Would I do it again? I'm not sure but I'm sure glad I did it once. These are the kinds of experiences I travel for. The memories I will cherish!