Mediasoup has a more low level API. It's more of a library/framework to make your own SFU (although there's an example SFU). Jitsi is more of a ready to use SFU. Mediasoup is newer, but has seen very fast development. Last performance comparison I know of had mediasoup as a clear winner over jitsi. But that's a fast moving target and the usual limitations of a benchmark apply here as well: https://webrtchacks.com/sfu-load-testing/

Mediasoup has a c++ core with node api. Jitsi is java.

If you're experienced with webRTC, you will probably like mediasoup better. Otherwise I'd stick with jitsi.