iBooks version / iPad
Every iPad including the original can run iOS 5.1 so it doesn't matter which iPad you purchase. The original iPad can be updated to iOS 5.1.1 and at the time of writing all other iPads (including all iPad&nbsp;minis) are still able to be updated to the latest version of iOS (7.1).

iBooks 3 requires iOS 5.1 so is able to be run on all devices that can run iOS 5.1 (therefore all iPads). However, iBooks 3 uses more system resources and the first generation barely handles it with numerous complaints of crashing simply because the first generation iPad doesn't have the resources available.

Ideally you probably want to buy the most recent iPad you can which will give you the ability to update in the future.