I'd say Terrans. Mostly because of the vasudans, as opposed to the Shivans.
Post-FS1, the Terrans were in worse shape because they had to suffer the damage of a significantly powerfull Vasudan fleet, and the fact was that they were actually loosing to the Vasudans (albiet slowly).
Now, the Vasudans were stronger when the shivans came, and took only a little more brunt of the damage to their military, with the major loss being their homeworld. However, post-fs1, they'd still be better off than the Terrans. Not only were the Terrans weaker at this time, but they pretty much lost an entire system, as opposed to a single planet. Vasuda would have been recaptured and probably re-colonized as well, with the system still minable at the very least. Their military would also still be intact, with all losses at least recoverable.
The Terrans pretty much lost a significant system completely, a significant portion of the military in that system as well as the resources available in it. Remember - they must have been preparing for a blockade, which means that a significant percentage of the GTVA's ships would be at Earth. The Vasudans would have already shifted their command and other centres off Vasudan when the Shivan advance came in, the Terrans had to build one anew, as well as everything else. With fewer systems than the Vasudans now, they would also be on the lower end economically and resource-wise.
Post Fs2 is a different story alltogether though. Here, it's pretty much a tie. Both races lost a significant percentage of ships to the NTF. The terrans lost two fleets, while the Vasudan ships would have fallen to the inital surprise attacks and the war of attrition that came later on. They would have also lost a significant amount of force to attacks against the NTF, since the Terrans would have been unable to assist till the fleets in other systems came in. This is nothing to say about the situation on the ground. Judging from human nature and brutality, the scenarios on Deneb and other worlds would have been catastrophic, to say the least.
To the shivans, both races lost a significant and sizable force, with the terrans edging the Vasudans slightly with the loss of several great-war era destroyers as well as most of hte Aeoli cruisers. However, this edge isn't much.
In the long run however, the Vasudans would have lost the most, as with the new Knossos technology, the prior loss of Earth incurred by the GTA would have been nullated. The fleets and ships from there would provide Terrans with significant advantages and resources over their Vasudan allies......