Since you can't use an ability/move to trap them in battle (they both have Roar), you have to give them status problems. The best you can get for HP is down to 1 which you have done. Second, status problems. Entei will be easier to catch than Raikou as Frozen, Sleep and Paralysis are more effective than Poison, Burn, etc..
Timer Ball should be quite effective - if not more, than just as effective as an Ultra Ball. Also, if you know you are about to ecounter one of the dogs, save before you do so. ou can turn off if you fail, that way. If you accedently defeat one of them and you did not use the saving tactic, if you defeat the Elite Four [again], they will reappear.
As always, the Master Ball will surely capture one of them - but only use it if you SERIOUSLY can't capture it. In a contition like this, you will just need persistance and patience.