I doubt you are going to find a 3rd party iOS application that will process cc transactions and let you send the result back to FM Go. There are a few like Square but due to PCI compliance I'm sure they are locked down.
You will need to come up with a way to run transactions from FileMaker. There are a few methods. I have one, sorry for the plug, CCQ-FM. It works without any plugins and is PCI Certified.Another option is to use a web page, linked to your FM db to process transactions.
Unlike the desktop where you can plug in a USB mag stripe reader and it acts like a keyboard extension you can't to that on iOS.
The mag stripe reader needs to be programmed to a specific program. We created CardSwipe to solve this problem.
You can read about both at www.ccq-fm.com
This might lead into the right direction. I use a iApp as a middleware to controll and read the swipe-reader to get the Card-N° into FMGo. The iApp get's prompted by a open-URL task in FMGo, the iApp set's a Vars that can be pasted into FMGo field.
There should be iApps which also deal the transaction-request with the payment-service.
Also check solutions like GoPayment