You can't catch Kyurem in it's White-Kyurem or Black-Kyurem form. Before you can catch Kyurem you must battle it in either it's White-Kyurem form (White 2) or it's Black-Kyurem form (Black 2). After you defeat it you need to go to the Dragonspiral Tower and catch either Reshiram (White 2) or Zekrom (Black 2) before you go back to the Giant Chasm to catch Kyurem.
Now with that being said I'll answer your question best I can.
Kyurem and Cobalion both have a catch rate of 3. But honestly if you only have one Master Ball I would use it on Kyurem. Basically because when you encounter Kyurem it will be at Level 75 while Cobalion will be at Level 45 unless your failed to catch it the first time then it will be at Level 65 when it reappears after you've defeated the Elite 4 . Because Kyurem is quite a High Level it can do far more damage to your team than Cobalion can. As well as this Kyurem is far harder to weaken if you don't have any Pokémon over Level 80. It also has the Pressure Ability meaning that your going to lose a lot more PP than you would when battling Cobalion.
To catch Cobalion go to Route 13 and Save the Game before you battle it. Make sure you have plenty of Ultra Balls and Timer Balls. A Quick Ball can also be decent if it is used on the first turn of battle (I caught a Palkia in a Quick Ball first turn) and Dusk Balls are also decent if it is used at Night.
First turn of battle I would throw a Quick Ball to see if you got lucky and caught it first turn. If not weaken Cobalion to low HP perhaps by using a Pokémon with the Move False Swipe and try to either Paralyse it or put it to Sleep. After that throw Ultra Balls or Dusk Balls (If it's night). Save your Timer Balls for last because the more turns the battle has the more effective the Timer Balls will be by the time they are used.
Hope I helped :)