Square and Paypal are two common options. As treasurer of a small non-profit myself, we use these two. PayPal's rate is 2.9% plus $0.30 per transaction, which we use for keyed transactions. We also have a Square card reader for swiping, which costs 2.6% + 10 cents per swipe.
I recently looked into Venmo, but it is for person to person only, no businesses (including non-profit.) I also looked into high-interest savings accounts but Ally, Capital One, and Discover are all individual only, not business. Sigh.
If anyone has experience with something else I'm interested in learning about it.