Lugia can be countered with Encore or Taunt quite easily. Substitute also does well. And of course Spore could be a viable counter. Lugia has 5 Weaknesses, and most of them are fairly common. Ghost, Dark, Electric, Ice and Rock. I find ice shard to be a useful check on most teams due to the abundance of 4* weak Pokemon with glass jaws and high speed. Rayquaza, Salamence, Dragonite, Garchomp... these all appear frequently enough to merit a check on any competitive team. conveniently enough, Ice Shard could be just what you need to finish off a Lugia before it can roost.
Also, pay attention. After Lugia Roosts, it loses it's flying type, so try to use a turn to set up shop by boosting your Pokemon on these turns.
I have never experienced trouble from a Lugia, to be honest. I see it most viable on an entry trap based team, so you could always counter it with a rapid spinner as well.