Payment Gateway Based Fees and Discounts for WooCommerce allows you to setup fees and discounts based on the payment medium selected by the user.
Apply Fees or Offer Discounts based on Payment Gateways This plugin lets you add fees and discounts based on the payment gateway. Fees and discounts can be applied globally or at the product level. The plugin can also apply fees based on country, state, product category etc. The plugin also provides the ability to apply taxes on fees. Fees can also be calculated by excluding the shipping charges if needed.