It doesn't matter what Pokeball you use. If you have the Master Ball left over, you could use that to catch Latias. However, Ultra Balls will work the best if you do not have the Master Ball.
I'm guessing you don't have a Master Ball since your asking this question, so the best ball to use would be an Ultra Ball. Sometimes it takes more then once to catch a Pokemon, so you just have to be patient and try not to freak out like me when Latias runs away after chasing it for hours. :D
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after that, someone at the battle frontier will tell you about latias and latios. then, latias will start roaming kanto.
In the pewter city museum. to get his attantion you must bring walking latias ( heartgold) or latios ( soulsilver ) with a soul dew from a mystery gift. then he will take you to saffron city. he will talk to you for a while. then he will go back to pewter then show you latios ( heartgold ) or latias ( soulsilver ) outside of the museum. then after you defeat or catch one of eon Pokemon that's the last of him.
a Master ball or alto of ultra balls
Just be paitent and catch it with a pokeball!
I would recommend that you use on latios or latias w/e which they are because raquaza and kyogre are fairly easy to catch You don't have to use your Master ball on anything. You can use it on Kyogre, but that's the easiest legendary to catch, so I don't recomend it. You could save it for later on, like for Rayquaza. That's MUCH harder to catch! It's at level 70 when you encounter it, but you could still catch it with a normal Pokeball (I did). And then, you could catch Latias with it, which would be the best in my opinion, because unless you have a Pokemon like Wobbufett, with the ability Shadow Tag that doesn't let the opponent escape from battle, then it would be pretty hard to catch. So I say catch Latias with your Master ball.