I tried to measure which was better a while back, thought I'd share.
All damage was done against a lvl 60 training dummy in Stormwind. Keep in mind that I didn’t include poisons (Im usually running double cripp anyways) but did make sure to include the same number of crits and non-crits in my averages.
Daggers:
Backstab – 57.6 average hit
Ambush – 115.8 average hit
5 pt Eviscerate – 111.5 average hit
Swords:
Sinister Strike – 24.9 average hit
Ambush – 111.5 average hit
5 pt Eviscerate – 110.6 average hit
In a normal rotation you would:
Sword – ambush + 3 sinister strikes + eviscerate = 296.8 average damage / 130 energy = 1.29 damage/energy
Dagger – Ambush + 3 backstabs + eviscerate = 400.1 average damage / 275 energy = 1.45 damage/energy
1.45/1.29 = 1.124, meaning daggers do 12.4% more damage than swords
Weapon swap macro to swap between Sword and dagger for MH to burn energy on SS's if you can't get back.
Build equip dagger into your stealth key as a macro
Macro to use SS if swords are equipped and BS if daggers are equipped.
Be careful with the SS or BS macro though. If you have a dagger in your offhand then [equipped:daggers] will flag as true so you want it to be something like