1) Square, because they have no fixed fee per transaction. 2.75% means 27.5c per $10 charge. It's not really something you integrate with an app, but with talking of swiping, it's not clear what the use case is.
2) PayPal micropayments. At 5% + $0.05, it's 55c per $10 charge. PayPal has a card-swipe reader the same as Square, but people can also pay with their PayPal accounts, or you can take full control over the payment interface by implementing the PayPal Pro API in your app.
Both are less than the 2.9% + $0.30 offered by Stripe, Braintree, or most any low volume MOTO merchant account.
I don't think anyone can recommend what the best input method is without any knowledge of what your app is or who your customers will be.
They shouldn't be compared to PayPal, Stripe, etc. but to the standard merchant accounts brick-and-mortar stores get.
If it goes through the iTunes store, you're required to use Apple's payment system.
Are you looking for the cheapest, the easiest or some combination? Stripe seems like a no-brainer.