I found this comic book app for iPad called comicpad.
http://www.denvog.com/iphone/ComicPad/index.html
I downloaded it and the current version doesn't allow you to download your personal CBR, CBZ file using iTunes. But I have heard that the developer has submitted the latest version to App Store which will support iTunes syncing. Till then you can try and see if it works for you.
cheers.