The Gaffer's ability looks at how much life you've gained in the turn, even if it wasn't on the battlefield when you gained life. It doesn't care if you also lost life, even if you lost more life than you gained.

You draw just one card, no matter how much life you've gained past 3 life.

If you haven't gained 3 or more life by the time an end step begins, The Gaffer's ability won't trigger at all.