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 me
A sense of obligation."
The men in the boat might be struggling for survival and cursing the universe for their situation, but nature, like the tower, sits there with zero care.
In my opinion, the sea represents the same kind of indifference. I remember reading this story the first time, and I remember being upset at the ending. I had just read an entire story that painstakingly told a story about the heroic efforts of four men to make it ashore. I found myself willing all of them to survive. Then the end of the story happens, and readers learn that the oiler still dies. All of his efforts were for nothing. The sea simply didn't care how much he wanted to live and how hard he worked for it. I suppose that the sea could also symbolize death. The men in the boat know that their safety is found in the boat and on dry land. If too much of the sea gets in the boat, the boat sinks and the men die. If the boat capsizes, the men likely die. If anybody falls overboard, that person will either drown or be eaten by sharks. Staying out of the sea is critical for living. Being in the sea is a death sentence.
Finally, the gulls. I do think they are also symbolic of nature's uncaring eye on the men in the boat; however, I think they are also symbolic of death as well. There is one paragraph in the story that is intensely focused on the gulls, and the words used to describe the birds all hint toward a future death in the story. The men in the boat seem to sense that about the birds as well because once the birds are frightened away from the boat, then men have a sigh of relief.
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.