I do not know which to prefer, The beauty of inflections Or the beauty of innuendoes, The blackbird whistling Or just after.
You might have noticed that the poem has gotten more abstract and symbolic as it goes along. In this section, the speaker is of "two minds" (see Section II) about whether he prefers "inflections" or "innuendos," which correspond to the sound of the blackbird whistling and the silence that follows it, respectively.
"Inflections" and "innuendos" are presented as contraries or opposites, but, strictly speaking, they aren't.
An "inflection" is a sound that changes in tone. Birdcalls are full of inflections. An "innuendo" is like a hint or suggestion, something that is implied but not stated outright. In this rather complicated metaphor, the silence "just after" the bird whistle is like an "innuendo" because you can still hear the whistle in your head even as the sound has died away.
Once again, this isn't chemistry – there's no right answer about what these lines mean. They are more like food for thought.