While I don't particularly disagree with any of these posts, I would disagree that Edwards used these metaphors strictly to instill fear in the hearts of this congregation. These are strong images because that's what it takes to awaken hearts which have been dormant and unproductive. While it's true that those who have turned from Him deserve His wrath (and those are the images we see and hear so often in connection with this sermon), the entire sermon is spent reminding them that He is holding back His wrath. He has not released the arrow, His open hands are keeping us from falling into the pit. Storms (and weather imagery of all kinds, for that matter) are common literary symbols and would have been well understood by this group.
Black clouds are foreboding, signaling a great thunderstorm. a storm that often brings destruction. This metaphor is used by Edwards in order to unnerve the congregation and inspire the threat of punishment for their sins from the God that is "dreadfully provoked."
Great answer! I think that line is also an allusion to the flood in Genesis. The black clouds might remind the congregation of storm clouds and the great destruction of the flood. Edwards used many biblical allusions, which added to his credibility in the minds of the Puritans. Edwards also used a lot of natural imagery like floods and fires to frighten the Puritans with images they would have been familiar with.
This famous Sermon came as part of the "Great Awakening" in Enfield, CT. The community at Enfield was a particularly difficult group, resisting the call to conversion. Edwards used direct appeal to emotions to attempt to reawaken the their religious fervor. The gist of the speech is that God, who is VERY dissatisfied with this particular congregation (hence the "black clouds of God's wrath") holds each of the congregants over the flames of hell, suspended by a thread (think of a spider held over a fire) and the only thing that kept them from being cast into hell is his will, pure and simple. Nothing they have done can keep them from the flames; only His will kept them alive for even another instant. But there is no guarantee that they will not be dropped into the flames at any given moment should God so decide. The sermon is known for the vivid imagery that it employed and it is reported that it was particulary effective, with reports of weeping and hysteria in the pews.
For more information see http://www.enotes.com/sinners-hands-an-angry-god-salem/sinners-hands-an-angry-god.