We push cash or check as our preferred forms of payment, but use Square and PayPal as necessary.
Reservations made online via ResKey get routed to PayPal for payment of the confirmation deposit. Most of our reservations come by e-mail or phone, though, and for those who want to use their card, we tell them we are not set up to take credit card details securely over the phone, but that we can e-mail them a link to a secure site online where they can enter their payment card details (via Square's invoicing feature -- since the user entered the card details themselves, we are charged only the "card present" fee rather than the higher "card not present" fee).
We have put in a pre-order for Square's new "chipped card" reader -- it's not free like their "mag stripe" reader, but very reasonably priced ($29) -- so we will not be assuming liability for chargebacks on chipped cards.
Our bank offers a processing service very similar to the Square, and at essentially the same rates, but I suspect they are somewhat behind Square in terms of rolling out features and capabilities (I don't think they offer the online invoicing, for example). The only advantage I could see was that we might get the money into our account a little faster (maybe). I balked when they required that we sit for an hour or two of "training" before they would activate our account....