All day thy wings have fanned, At that far height, the cold, thin atmosphere, Yet stoop not, weary, to the welcome land, Though the dark night is near.
Okay, then—now that the speaker has suddenly stumbled upon a lens through which to understand the waterfowl's seemingly pathless flight, he takes things a little further
First, however, he starts with another description, as he did in the first stanza.
The waterfowl's wings have spent the entire day fanning (the speaker's word for "flapping") the "cold, thin atmosphere." That sounds exhausting.
The phrase "at that far height" describes the location where this whole fanning business is going down. Now, we know this phrase is kind of jammed into the middle of the sentence here, but that's to be expected.
As in the first stanza, the speaker is showing us yet again that he's hip to the whole stream of consciousness thing, and sometimes just says things as they occur—even if that is, well, a little confusing.
So, the waterfowl's wings have spent the entire day fanning the cold atmosphere of the sky. This is a very laborious task. Just try going outside when it's really cold and moving your fingers for an entire day, and you'll have some sense of the bird's crazy endurance.
Even though the bird must be tired from all this flapping, he doesn't "stoop […] to the welcome land." He just keeps on flappin'.
The land is "welcome" because, well, after a long day flying around, why wouldn't a nice place of rest be welcome? We don't know about you, Shmoopers, but we'd have come in for a landing hours ago.
Not this bird, though. The "dark night" is approaching, the speaker says, and it should be time for the waterfowl to return back to the "welcome land." Apparently, the waterfowl doesn't want to return.
Now, "dark night" definitely refers to the literal night that comes after the sunset (remember the first stanza tells us that the action is taking place at dusk). But it may also be a metaphorical reference to the "dark night" that is death (not Batman—that's the Dark Knight), the time when all the proverbial lights of life go out.
We can't be certain if the speaker is talking about death, but something about calling it "the dark night" makes it seem kind of absolute, like he's talking about a very specific "dark night" that all of life will one day experience.