what pokemon

You should use your masterball on Entei. Why? Because you can try and catch Mewtwo whenever you want, but with Entei you have to find him, and when you find him just throw the Master Ball.

Hope this helps.

Entei would be the better choice.

To catch Mewtwo just save the game before you battle it and then try and catch it but make sure you have a lot of ultra balls and some timer balls. Timer balls can be obtained on Two Island and are great for catching legendaries as they have better success the longer the fight is so don't waste them at the start of the battle. Hope this helped good luck on catching both of them
Fireguy

You should use your masterball on Entei. Entei will just flee after one move you make so if i were you i would choose entei1 If you also want Mewtwo you should get lots of timer and repeat balls. Just get some ultra balls just in case. Reminder: Your pokemons have to be at least level 69 to weaken mewtwo.

If you have a wobbufett,use it on Mewtwo,if your Pokemon aren't level 70,however,if you don't,use it on Entei