Brian - we use AffiniPay (and love them). We used the card swipe into a custom form that they created for us at the last major conference, but would use it more if there was better integration. We primarily use it for on-site payments and store transactions. We only use Macs, so that is very important to us in what you are implementing. A couple of problems I see:
1) the payment portion of the registration process is far too rigid (fields required, optional fields, etc.) for these methods
2) with the new iPhone 7 (and later), there is no audio jack, so that will present a problem until the manufacturers offer a lightning port
Any help in making this process more integrated would be greatly appreciated and we would be happy to help with testing.