You will need a card reader compatible with the iPad, such as iMag Pro, and an iOS app such as CardSwipe. Then you will need a script within FMP that opens the app and receives back the swiped data using a URL scheme. See an example of this at http://www.ccq-fm.com/cardswipe/integration.html
Hey thanks Anders, I'm checking this out now.
Looks like will be a great learning process for a new type of solution, really looking forward to it.