The boys were throwing a ball. (Indicates an ongoing action in the past. Often this form is used when you want to contrast it to something else happening. The boys were throwing a ball when one of them missed and the ball hit the neighbor's window.)
The boys threw a ball. (This indicates a main action in the past.)
It could mean either. It is merely stating a fact that happened in the past. The sentence, "The boys were throwing a ball" gives more of a sense that it was something that continued on for a period of time in the past. The focus is on the continuing action.