I just did this trip so thought I'd share a couple of tips that I wish I had before I went.....
Catamaran is good option but be prepared for a choppy ride and even for the toughest of stomachs, you may get sick. My catamaran had about a 60-70% vomit rate amongst the passengers. I knew I was in for a bumpy ride when they passed out plastic bags to each passenger as the boat left port. So prepare yourself. Take some motion pills if you can. Also don't party hard the night before and be careful what you choose to eat/drink before the boat ride. Also I think best to sit on the external part of the boat so you feel the breeze and you can keep your eyes focused on the horizon. Don't close your eyes, look down or read. Just stay focused on the horizon and you'll have the best chance. Also, plan to get a little wet on the outside area. Even though it is in back, you get wet a bit from the splashes of the waves against the boat.
So if it is a nice day, the catamaran will go direct which takes about 2.25 hours. If the seas are way too rough, they won't say anything to you but will travel for about 50 minutes and you exit the boat at a pier. Then they will stick you on a bus for another 1.5 hours (still not saying much) then take you to another small ferry boat that will travel for about a half hour to Morro port. The full time on this route is 4-4.5 hours with the 2 boats, bus and time it takes to corral people through each transition. The reason I share this with you is so you can be prepared and less confused than I was. Also good to consider this when making your other plans (eg flights, tours) to give yourself cushion as you won't know if you go the short or long way until it is time to leave.
Of yeah, and I thought I was going to be clever and avoid the whole catamaran thing for my return voyage by taking a plane. I saw the website, read in book, saw ads around town about a small plane flight option for like 279 reis from Morro to Salvador airport. Perfect! So I got to the island, tried to book it and learned that the flights are no longer in service. Not sure if that's a permanent thing or just for the season but good for you to check in advance if you want to take the plane too. Best to get your hotel to check for you.