As someone who's done it, I like the bus. Of course, there are pros and cons of each.
Pros: A bus is cheaper, you get to see more of the countryside, interact with more people. You get breaks, get good seats (they have business class buses!), and you can stop off at places on the way. We stopped in Arequipa to go to the Colca Canyon, and in Nazca for a few hours to see the Nazca Lines.
Cons: It takes a long time. Some legs in the desert can be dull. Some people argue that it's a dangerous road, but I'd say that's maybe only in the mountains - the coastal road from Nazca to Lima is modern and high quality.
Pros: You get there faster. You get an aerial view. Save time.
Cons: It's more expensive. You will not have a gradual introduction to the altitude, and may as a result get a bit of a shock when you step off the plane - it can be quite hard the first few days. You're stuck in a cramped economy class seat. You don't get to interact with many people.
Hopefully that helps. Personally, even though I bused last time, if I had the time, I'd bus again. I disagree with @vartec - the choice is not obvious, and I loved the bus trip. But you must make that decision yourself, of course :)