As people who hear me speak know, I often point out that iF your nonprofit's website doesn't accept credit cards and PayPal, you've lost money. Period. The increasing number of people who are comfortable ordering online are less and less prone to want to write a check. In fact, fewer and fewer "checking account" customers, particularly under 30, EVER actually order checks from their bank.
Some older execs point out that credit cards cost a percentage of the revenue received (usually 4-6%), and I counter that 94% of something is better than 100% of nothing.
So what to do? TechSoup has the answers, of course. They always do on tech for nonprofits. Check out this article on the Techsoup website about credit card options and methods for your nonprofit. While you are there, make sure to check out TechSoup Stock, the donated (new) software available for nonprofits and libraries.
And, here's an article on selecting an online donation tool (software), also on the TechSoup site.