We decided to go with Skyline Payments.  They integrate with Quickbooks quite nicely.  I have been happy with them so far.  It is a whole system that allows customers to see their account balances, make partial payments, use credit cards or banking, etc.  It does cost about $100 per month for the software but the money I save on credit card fees makes it all worth it.  The technical support has been great too.  I am happy with them.