It's hard to say without seeing the covers. I have always used Sunbrella fabric for covers and have had good luck with it, but I don't know exactly what combination of materials are used to make it. I just had a full cover made for our Top Gun out of a new material that the canvas shop recommended. I don't know the name of it, but it is supposed to be the "new and improved" Sunbrella type fabric. Maybe somebody here will know the name.
One thing to consider is that the one with cotton may be softer on the finish of the boat, but I would think that it would shrink some over time. I am also thinking that the polyester may be more waterproof, but I may be wrong. If nothing else, call the manufacturer of each cover and explain to them what you want out of the cover. I would think that they could certainly make a recommendation.
You also mentioned that you will probably not tow with it. If you do, be 100% sure that the cover is tight and will not flap in the wind against any part of the boat. Like with the material selection, the manufacturers of the covers you are looking at may have a cover that will handle both towing and protecting the boat while it is parked. It certainly could not hurt to ask them.
Here are a few pictures of our new cover. We have had the same local company make several of these for different boats in the past and they do a great job. These covers will work while trailering or while sitting still. They keep the boat clean and protect the paint from road grime and debris. Custom covers can get very expensive, but if they are done correctly they are like having a garage for your boat that you can take with you anywhere you go.