I commute with a back pack. I have a small sling pack that goes cross my back and I use that for most travel. On days when I have to move the laptop I use the back pack. I wrap it in a plastic grocery bag of it's raining. So far no issues. My ride is fairly short (20 min).

I have had panniers before but I'm not sure I would be comfortable riding with the laptop in the panniers due to the possibility of water being splashed up by passing cars. My paranoia; maybe not yours.