I would say that the tower is the most straightforward symbol in the story because Stephen Crane comes out and writes down exactly what the tower symbolically represents to the correspondent.
It represented to the correspondent the calm of Nature against the struggles of the individual—Nature in the wind, and Nature in the sight of men. Nature did not seem cruel to him then, nor kind, nor dangerous, nor wise. But she was not interested, completely not interested.
The correspondent's view of what the tower represents is not shocking considering that Stephen Crane is a naturalist. Naturalism often will portray nature and the universe as completely indifferent. Crane's poem "A Man Said to the Universe" is a nice portrayal of the universe according to naturalists.
A man said to the universe:“Sir, I exist!”“However,” replied the universe,“The fact has not created in meA sense of obligation."
After it had been discouraged from the pursuit the captain breathed easier on account of his hair, and others breathed easier because the bird struck their minds at this time as being somehow gruesome and ominous.
Well, first of all, remember that this story was based on actual events and Crane a Naturalist who sought to evoke the world as it was. Therefore the details you mention need to function first and foremost on the literal level: the sea is first the sea (and only second anything symbolic), etc. Next, remember that the point of view shifts, and so these objects might mean different things to different people. To the news correspondent, for example, "This tower was a giant, standing with its back to the plight of the ants. It represented ina degree, to the correspondent, the serenity of nature amid the struggles of the individual—nature in the wind, and nature in the vision of men." That's a clear statement of meaning, but it isn't the only meaning. The others on shore seem not to care about the tower, almost not to see it. For them it means less.
As for the gulls, we're told they are "uncanny," and so they represent the weird and unpredictable: fate that could go any way. The sea is related; it is the power that determines the fate. It is the great unknown of nature.