Mamoswine. End of discussion.
Just kidding. Landorus is probably the easiest to deal with, as you can either outspeed and kill with a SE move or just wall it with a generic physical wall. Thundurus is a little tougher, as you can't simply beat it with Blissey thanks to Focus Blast, but the NP set can be easily outsped and the scarf set lacks power and struggles with electric immunities. Oh, and Thundurus makes a decent counter to itself, as you can absorb Thunders or Volt Switches and hit back with HP Ice. Tornadus is the hardest to deal with, as it can go mixed to beat walls and can take a hit from the scarf users that outspeed it. That's what CB Mamoswine is for. :)
Oh, and congrats on getting my 1000th VM!