In don't think there are any common practices for this yet. I don't think many organisations are archiving iOS apps, and I don't think anyone knows to preserve them! Certainly, I know I'm not the only one looking forward to seeing what MoMA does with Biophilia.
As for iBooks, the underlying format is a proprietary extension of the ePub spec. and, if you downloaded it from Apple, it will presumably be protected by DRM. If it is DRM'd, you may not have anything you can actually meaningfully archive (at least without breaking the law, depending on your legal context). If it not DRM'd, it may be possible to create an ePub version, but I don't know if any tools can do that yet (the most likely candidate would be Calibre).