i dont think "best" would be the appropriate term for any of the Factions, each has their own abilaties & Strengths
I Voted Slaanesh as i like the Initative Bonus i get, when i take it. their Legion Troops are cheaper then all other legion troops and can be taken as Fire support troops or as decent Assault troops with high Initative.
My Second choice would probly be Nurgle in particular their legion troops T5 with feel no pain is to good to pass up these things are nigh on indistructable when used correctly my only problem with them is that their Expensive so if you go for a pure force you end up with a fairly low model count.
3rdly Thousand sons, the fact that you have AP3 bolters means that even with a low model count if you rapid fire a unit at least have of the unit is going to go down (against MEQ's at least)
4th Khorne Beserkers these are my least favourite of all Legion Troops, sure with pleant of attacks these guys are killer in CC, Especialy on the charge, but if they receive the charge well they lose their Bonus and are Quite Vunerable.
over all if used in the combination any legion troop can be Deadly to any enemy. Combining legion troops is a very nice Tactic such as Plauge Marines and Khorne Beserkers.