Add an extra to the price of the product
We've covered this concept before in our "pizza store" tutorial, though it appears the video may not be online any more: https://drupalcommerce.org/videos/tutorials/customizable-products-pizza-store

The steps would be the same, though. I'd basically add a price field to the taxonomy vocabulary and then include the upcharge in the price field for the options the customer is selecting. Rather than using this taxonomy as a product attribute, you'd put it on the line item type as a custom line item field. Then you'd create a pricing rule that evaluates the fields on the line item type to look for a value in the upcharge price field and adds that amount to the unit price of the line item.

This is about as in depth as I can go on StackExchange. To learn how to use any of those particular features outside of getting this recipe, you should find real-time support at a local meetup or else in the Drupal Slack #commerce channel.