It's a tough one to decide. Both forces have some very high showings.
Personally, whoever wins is likely to be decided by how Shivan beam cannons and Reaper shields interact. If the particle beams slice right through the shields or at least have easy penetration like against other Freespace craft, they'll win. If the Reaper shields are powerful enough that they need to burn through the slow way, than I'd give it to the Reapers.