I would go with fed-UH-verse. The word Fediverse is a portmanteau of the words federate and universe, right? So if we're going with the US pronounciation of the words it's fed-UH-rate and you-NUH-verse, both have the "uh" sound in the middle.
Things get a bit trickier if we're using the UK pronounciation, though. The word federate is largely the same, but universe gets pronounced you-NEE-verse, so it could go either way.