If a JotForm is filled out on an iPad, is there a way to use a card swiper as payment?

Unfortunately, JotForm does not have such feature, I think this might be implemented, but it would require to add some JavaScript code, something that's not allowed on JotForm. 

However, you could get the source code of your form and try with the following link that may help you to connect a card reader to a web application: http://stackoverflow.com/questions/5243165/connect-a-credit-card-reader-to-web-application