I work for a NFP and the process was a complete bitch. We tend not to use external suppliers (eg GoFundraise or EveryDayHero) as they like to take a cut of the donation. Although these kinda sites are great for people wanting to raise money for their preferred charity.
We've also set up a NFP PayPal account again it was a nightmare for all involved - soo many forms and procedures.
I can ask our web dev team and post how they did it - when they respond?
I did contact stripe.com, and they came back with some decent fees, and there are a few Wordpress plugins that make taking donations via them very easy, so may go down that street. But the more options the better.
I know this was asked a while ago but just in case it helps anyone in the future.
I previously did work for a not for profit which used SecurePay https://www.securepay.com.au/. I know they got a good deal and SecurePay do run charity programs. Couldnt find any info on their site but i'm sure if you got in touch they could help you out.