At Hack Club, a 501(c)(3) nonprofit that helps teenagers run high school hacker clubs, we accept cryptocurrency donations at
https://hackclub.com/donate/.
We open source nearly everything we do at https://github.com/hackclub, even our finances. We have deeply appreciated the generosity of the cryptocurrency community.
We have a Coinbase account where we store received crypto. In our books, we log everything in USD and I believe we record our crypto holdings as an asset. This has worked at our current size since we are a small and cash-strapped organization focusing nearly all our efforts on those we serve.