It doesn't really matter if you are going to use the master ball to catch but if you are saving it for Mewtwo or groudon then any level above forty should work I suggest having a pokemon that can learn false swipe to minimize it's hp and a pokemon that can paralyze it. Then use a defensive pokemon like Umbreon and use dusk balls/Ultra balls. If you are trying to kill it then any strong rock, dark, electric, or ice type that is around it's level can defeat it easily.
Note: Lugia is a very very good pokemon that is hard to even damage when Ev trained and has a good set but the wild one is a pushover the only challenge is catching it.