The most significant differences between the two are on the back-end, undetectable by the user. From a user perspective, they are pretty similar although the interfaces and in-built controls have some noticeable differences. Try them both and see which one you like better.
Each instance is a server that someone set up that is running the software. You don’t have to worry about it too much; it’s not like Mastodon or something where the instance has a lot of meaning or significance. If you are streaming some videos and getting bad performance or it isn’t working, try connecting to a different instance. Each instance might have some slightly different settings, but nothing major.
I downloaded the LibreTube app from F-Droid, and it was good enough that I haven’t bothered checking out anything else. 
I don’t watch that many videos in the first place, so take that for what it’s worth.
Also in F-Droid, the UntrackMe app is pretty good for automatically redirecting links to libre front ends (so you can click links out of web search results and they open in your alternative front end automatically).