There's no real endgame DPS difference. They have the same DPS Augments and they'll both easily hit 99 STR for Masamune I. Biggest differences are:
In regards to DPS, probably 'staying alive' means more DPS, so:
- BSH/KNI big Magic EVA advantage (Zodiac Esc. + Shield Block 3) makes a Critical HP (Adrenaline) BSH easier to keep alive.... Technically, you have an even bigger EVA advantage but most hard bosses ignore your EVA as if it were 0
- BSH/MNK in theory would have more HP without Bubble (since BSH/KNI needs to wear pure STR armor; BSH/MNK can hit 99 STR with 1 piece of Light Armor for HP) but Bubble kinda nullifies this advantage
Stat wise:
- BSH/MNK has better late game STR/MAG pre-Masamune I because of the extra Battle Lores
- BSH/KNI has better STR/MAG growth early on because early-mid Heavy Armor usually has more STR than Mystic Armor has MAG (1 MAG very slighty > 1 STR but for most of the story choosing between the two armor types will probably be a a few more STR than MAG)
- Only BSH/MNK can hit 99 STR/99MAG... BSH/KNI will miss slightly except on Ashe maaaaybe Vaan. Basch and Balthier miss though. However, since Masamune I uses just STR it's kinda symbolic (I mean it's still nice for your KNI or MNK heals but you're BSH is probably Berserked anyhow)
BSH/KNI is better IMO for the extra Magic EVA, but it's pretty marginal. As long as you got 99 STR and Adrenaline, you're good to go. I personally still went BSH/MNK just because I had nowhere else to put MNK (but I needed Whale Whisker with a Genji-user) and I already had 2 KNIs anyhow (and all 3 of my main characters use shields and I wanted the 2 characters to use Zodiac Escs. that I got without using Trials to get a 3rd -- no Trials items on my main file). But if I was designing a perfect 3-man party, I'd have given the edge to BSH/KNI so I could give him a Zodiac Esc. with Shield Block 3. I think it's worth it to help a Critical HP or Full HP BSH stay there a little more consistently.