Most tournaments nowadays accept electronic payments using PayPal. And in most cases, the relevant PayPal link is listed in the NAGVA website. Here's how to find the link (and also see if other payment methods are accepted):
Step 1 - On the blue horizontal menu, click on "Tournaments".
Step 2 - On the left hand side, select the tournament you want to pay the registration fee for.
Step 3 - On the left hand side, find the box called "Payment Details". This box contains instructions for each accepted method of payment (e.g., where to mail a check), a PayPal link that will take you to the tournament website and, occasionally, an embedded pane that allows you to add the registration fee to your PayPal cart.
Important note: Make sure your team is registered for the tournament before paying registration fees. Tournament directors and registrars must be able to identify what team you're paying for in order to process your payment appropriately!