This article will walk you through disabling payment methods for certain products.
First go to Tools > 3 Power Features > Custom Field Setup then click New
Now add new field named "Payment Methods Disabled." It needs to be created with Field Type= Products, Input Type = TextBox and Value Type = String.
Now on the product editor enter the payment methods you want disabled as a comma separated list. Enter the name exactly as it appears in the dropdown box on the checkout page. (Do not include any trailing or leading spaces) ex: "PayPal,Credit Card"