I bicycle commute with my laptop daily and found the Topeak laptop bag is the best solution for me. Note I'm not affiliated with Topeak in any way. Another bicycle commuter at work noticed my set-up and now he has the same for his laptop. The following is a link to the bag on the Topeak site.

http://www.topeak.com/products/Bags/MTXOfficeBag

My normal commuter bikes (Surly Karate Monkey, Novara Strada) have the Topeak rack which makes taking the bag on/off quick and simple. I've also used the bag on my Cargo bike (Trek Transport) with a non-Topeak rack and some bungee straps. Amazingly the latch still functioned on the Cargo bike but needed the straps to stop the bag from wiggling. I've had a few opportunities to test the rain cover here in Texas and can report nothing inside the bag got wet including paper. It comes with a shoulder strap. I now use the bag to always carry my laptop independent of commuting by bike or car.

The downsides are it's a little pricey depending on where it's purchased (got mine at REI), and there's not a lot of room for other stuff such as a change of clothes or lunch. I end-up using a bungee net to hold my lunch bag and/or dry bag with change of clothes, on the top of the laptop bag when needed. The upside is I'm still the widest thing on the bike and the bag stays out of the wind as opposed to a normal pannier set-up.