Actually, I typically use the IC thread itself to post pack-link conversations, at least when the information is something the character(s) don't care about others seeing in an OOC way. There is really no harm in it, as long as the pack-link portions are clearly marked as such (i.e. between <PL>, [PL], <PML> type brackets, "Said over pack-link:...", etc.)
The main benefit of keeping things in-line with the thread, is that there's no mistaking when things are said. When things move to email, IM, PM, private boards, etc., you have to resort to looking at time stamps, and must rely on clear communication from the other player setting-up exactly when a specific thing was pack-linked in relation to what others are doing/saying in the scene.
I do not, by any means, have any preference for how individual players want to do it- that is their prerogative. For me, it's just easier to keep everything together in the thread.
For the record, any pack-link conversations that are NOT clearly marked, may be ruled by an ST to be "said out loud," so mark your posts as clearly as possible!