I disagree that the fact that crocodiles, and alligators are freshwater should matter, it is a game, and they are allowed a certain amount of creative license, as for zombies, while I agree they are very common, especially in the crafting genera, there is a reason they are popular, they are almost always a threat, although usually not an unmanageable one, and they are fun to kill.
Bigger sharks, and squids would, in many ways, be more of the same, they would be a threat in the water, or to the raft, but at this point, either of those would just a boring annoyance, or would fundamentally break the game, we need an enemy that challenges you in a way the shark does not in the mid-game, something that is more a threat to you then the raft, because honestly, your raft is pretty secure at this point, and you don't really want that to change.
As for seals, I think they would be bad because people would not want to kill them, seals are generally seen as cute, and sympathetic, and having to fight them would probably not do the games favors.