Well no, there are ships, but they are so old none of them are sail worthy.
http://www.brinkthegame.com/media/concept-art/
The concept image 3rd from the right, 1st column.
Security Personel definitely have access to an assortment of sea worthy craft, as well as helicopters. We can probably assume that the Resistance Fighters have atleast a small number of raggedy fishing trawlers, or other ships of the like, but definitely not anything substantial.
Regarding the topic, the game was designed so as to allow for either idealism to be correct. It was done in this manner to give the player a reason as to why he was fighting: a motivation. In my opinion, it is the Resistance who are at fault. They are, after all, humble guests upon a construct of another's belonging. Their cause, to utilize the ark's remaining resources in order to reach whatever is left of the world, is a ridiculous venture. If there were any souls who had survived the rising seas, they would have come in contact with the ark. It seems to me as though the Resistance resembles a mass of home sick children ( :cryvaultboy: ), who are simply to stubborn to realize that nothing remains of their home. They ought to simply get over it, and help with the preservation of humanity's last remaining nest egg.