That is a difficult comparison to make. Ideally, you would have both.
If I was in your position, and had removed all fish to fight a HA problem, I would keep tank dark (including ambient/sunlight) for several weeks while skimming heavily. After a week or so of darkness go in there and scrub and siphon out as much alage as you can. Repeat this several times, all the while skimming as aggressively as possible. At the end of it all, do a large water change and see how your nutrient levels are.
How is your skimmer working? Does it take out much skimmate?