Most of the comic books released on the iPad and iPhone have been inside of special apps (many of which are run by ComiXology, actually), but here's another option. Comic book publisher IDW is set to release some graphic novels and comic books through iBooks, meaning that you can buy them right inside Apple's official e-reader app. 20 different graphic novels are coming out in the first round, ranging from genre stuff like Star Trek and Doctor Who, to licensed titles like Dragon Age, and older stuff like Locke & Key and Bloom County. Each should cost around $6 to $10 (which is competitive, especially compared to buying the full paper editions of these books), and should be available in the iBookstore soon, if not already.
I used to be a die-hard paper book reader, but lately I've seen a lot of value in iBooks, not just in terms of price, but also in the convenience of having all the books I happen to be reading stored on my iPhone. I have a feeling that ComiXology and other apps like it will probably remain the best way to pick up day-one releases of periodical comic books (at least until NewsStand comes along in iOS 5), but for library editions and collected graphic novels, iBooks could become the best and easiest way to read those.