Over the years I've used both panniers and backpacks. There are a billion variables so it's difficult to say which is best for you. I keep both available and for ME, the equation is:

big gear = panniers
little gear = backpack

I prefer to use just the backpack because it gives me more mobility on some of the rougher parts of the commute - but that may not apply to you. I find it's great for my day-to-day stuff like clothes. For heavier stuff like my laptop I prefer to let the bike frame do the work, so it goes in a pannier if I need to commute with it.

So my recommendation is to get both. You'll be glad you have the flexibility of choosing depending on what you have to carry on a particular day. Whatever you buy, spend the extra $$ if possible and get good quality stuff. Panniers especially will suffer the abuse of the road. And if you get a backpack, get one that is designed for bike commuting.