“Using the word vineyard would be wholly inappropriate.”
Opinions, it would seem, vary.
No one tramples on a vineyard, other than vandals or a herd of elephants, and clearly neither of those fit the meaning. They do trample on grapes, at least in traditional winemaking technique. People do so to "trample" on grapes to squeeze juice for fermenting into wine. In the narrative of the song the Lord is producing a result as well. War, in this case. As in “He hath loosed the fateful lightning of His terrible swift sword.”
Furthermore, as has been pointed out to you, within the words “He is trampling out the vintage where the grapes of wrath are stored” “where" refers to the second half of the line, not the first. Thus the meaning is “He is trampling out the vintage at the place where the grapes of wrath are stored.”
It's quite obvious.