Taking the ferry from Manila to Coron can be a challenge but the good news is the transportation system, namely the ferries, are slowly getting better. Coron, while popular for tourists, is still a small island group with a limited amount of Filipinos living on it. Ferry companies mainly cater to locals, not tourists so we are the after thoughts in many ways.
No matter who takes you to Coron, you will end up at the same place and it will be a overnight trip. Some of the boats are nicer than others and some are cheaper than the last one. The other factor is where in Manila Bay they leave from. There is something to serious consider.
There are benefits to taking the ferry from Manila to Coron over just jumping on a plane (Philippine Airlines, Cebu Pacific Air, and SkyJet serves Coron). You save a night in a hostel, you can relax and unwind and just gather yourself. There is also the factor that ferry travel is normal much cheaper.
You have to figure out what works for you and do what benefits you the most. For me, I enjoy the ferries in the Philippines and I do not mind the long trips too much. (I have done that marathon ferry from Iloilo to Puerto Princesa too!)
Ferry from Manila to Coron: Companies
The first one is the largely commercial option that is called 2Go Travel. They run twice a week (leave Manila on Tuesday and Fridays) to Coron on their way to Puerto Princesa and back to Coron on their way back. They get to Coron early Wednesdays and Saturdays and they and they come back the next afternoon picking up people heading to Manila.
The ferries themselves are quite nicer than the other companies and they have much bigger ships (and faster). It is a full blown commercial operation. They run everything on the ship at premium prices to get your money. Of course, prices in the Philippines is much different than prices in the United States or Europe. A basic ticket starts at around $25 and goes up from there.
The next option would be Atienza Shipping. They are a company that is mainly for the people of Coron. They leave towards the weekend. (Ask your hostel to call them to confirm. The number is 2 986 3118) and it is a 16 hour trip from whenever you pull out of Manila. The last time I made the trip, the cost was P1,100.
They have a few older boats that are used to mainly move produce and livestock from Palawan to Manila for the people. This is a great way to meet some real local people in the Philippines that are not somehow connected to the tourism industry.
The third option that I know of leaves from the same place that Atienza Shipping leaves and also leaves around the weekend. It is called MV Sea Journey. It is an older fishing boat and it goes to Coron and then to Cuyo. This is the also the link to the Cuyo Group without going through Puerto Princesa. They are also P1,100.
The only way I know to find out the information about them to go down to the booking station and ask them. They operate very similar to the other company but they just go to Cuyo instead of Palawan Island. That’s the only difference. However, like most locally owned companies; information is not easy to come by.
Security Concerns exist
As I said, both the Atienza Shipping and MV Sea Journey are in the same place and that is called Basco in the port of Manila. It is not safe by any means. It is a very rough area and even if the ship leaves late, I would be by sundown if you are not familiar with the Philippines or are a risk (women and children). Basco has been that rough for a very long time and that will not change anytime soon.
A mixture of extreme poverty, drugs, drunkenness, and every other addiction has left people in some pretty desperate conditions. They could see a white person walking down the path after dark as an opportunity to make some money for a fix or even some food. It is basic security measure to consider in an area ran by crime and drugs.
2Go Travel is on the other side of the port in a secure facility that are armed guards. As a commercial venture, they have an image to protect and because of that, the safety concern is not as serious as with the other companies. However, the cost of the security is built into your ticket so you pay more to use their ferries.