There are a number of commuter-specific panniers out there - In general, the common feature is that the padded laptop sleeve is inboard, attached to the stiffener panel, so even if you fall over, the laptop generally won't be bouncing off the pavement (which is a potential problem with a laptop sleeve in a regular cargo pannier.)

Some of these are water-proof, or so water-resistant they may as well be - the ones that are not generally have rain covers available, and I'd recommend getting one. If they're neither waterproof nor have a rain cover available, I'd skip it. Sudden downpours happen.

People who make commuter panniers:

Arkel
Ortleib
Vaude
Jandd
Carradice
Knogg
North Street Bags (Laptop sleeve is a $10 option.)

I'm sure there are others I'm forgetting...