I don't think I have what amounts to a full answer to this, but I have experienced the idea of "Anarchist Federations" as being an organization made up of various local groups (and sometimes groups organized along shared interests) which hold to certain shared central doctrines or political tendencies (examples here would be Love & Rage, NEFAC, Black Rose Federation, etc.) I've never been part of a federation, and I expect they wouldn't want me, but my observations are that they tend to have things like platforms, formal membership (sometimes including dues), and so forth.
Communalism would seemingly imply much more autonomy to the communes (local groups), who then establish connections between each other as appropriate. So, perhaps less centralized? Largely speculation here. Some folks wanted to start a federation where I lived years ago, and a lot of other folks who were already doing shit decided we didn't want to be assimilated into their borg that didn't necessarily represent or reflect our politics and motivations. We ended up with an "association" which later devolved to a couple collectives writing political things and a bunch of folks doing what they had always been doing without regard for the political shit. Which is to say I am biased, but maybe against both ideas?
I would love to hear on this from folks that have either been involved in one or the other form of organization, or that have historic perspective I don't (was/is the FAI as a federation different than current federations? How does Bakuninist communalism differ from the communalism at times espoused by Bookchin?)