Won of the best Pokemon to counter weather imo is Breloom. Breloom can easily handle Politoad, Tyranitar as well as most Ninetales pretty Effectively and when Techniloom gets released on wifi etc he will a top contender to take down weather.
The best anti-weather pokes right now imo are Breloom,Virizion,Abomasnow and Volcarona.
Breloom can eliminate every single weather inducer,allowing you to put your own weather or just remove the weather if you use a weather move.
Virizion can again kill every single weather inducer while at the same time being able to take hits from the more common inducers(Ttar,Toed).
Volcarona can again kill every single weather inducer and can even function in rain with its weather abusing set.It is so fast that it can outspeed even some of the Chloro sweepers like Victreebel and Tangrowth.
Abomasnow is not counted in the weather group because i don't really see him being used as a weather inducer,but rather than an anti-weather mon.
While it cannot switch in many of the weather inducers,it can threaten all of them with a physical set,while at the same time removing their weather...
Altaria can be a great ant weather. With cotten Guard it easily can be more bulky than gliscor. It can also with its added defense stack up DD dances. She works best in Anti Sand storm which most are physcial attackers
Breloom doesn't beat any Ninetales, except for the ones that switch in on focus punch, nor does he like directly switching into a specstoed ice beam. Let it be known that CM Virizion loses to Ninetales one on one. Volcorona also fails to outspeed Victreebel even after a quiver dance, and is promptly removed from the battlefield by either victreebel or tangrowth after a boost (tangrowth doesn't even need a growth/sword's dance to ohko you). Altaria doesn't help against any weather save for NU sun, due to the fact that its just too weak to hurt anything before boosting up and won't like being smacked down by a scarf landorus, ice attack, etc.
This mindset won't get you anywhere if you mean to want to defeat enemy weather teams as thinking like this creates the delusion of what it is that you're actually losing to. There is no team out there that actually fears Ninetales itself, nor is there any team that has to worry about being countered by a politoed (no, not even the mono fire teams).
You should be looking for ways to dispatch the commonly used pokemon who abuse the weather as the inducers are all relatively lousy and mediocre pokemon (save for tyranitar, but a special defense set gets you nowhere). What do I care if breloom just killed politoed? Now a LO Starmie is going to turn him into an appetizer, consuming the rest of my team as the main course.
The snowman has already been mentioned, but we should be looking for more pokemon like him. While I still consider him an inducer, he gets a nod for being able to successfully threaten the abusers used on all three weather teams. There are no sun, rain, or sand pokemon who enjoy switching into a moveset of ice shard, wood hammer, earthquake, and hp fire. The chlorophyll pokes don't like taking ice shards (and scarfsnow outspeeds them all anyway) while the steel types on rain teams no longer have the cover of drizzle to protect them from hp fire.
A few more things. If anyone is talk about slapping a weather move onto one of your pokemon (which has already been done), please do so only if you gain any benefits from it. Hail doesn't actually do anything for tentacruel aside from removing his leftovers and letting everyone know that you read a pretty awesome warstory. A bulky sunny day venusaur/tangrowth will annoy rain teams a hell of a lot more than this tentacruel ever will. A rain dance kingdra makes drought teams piss in their pants if you're able to bring kingdra in on Ninetales. If you're still using tentacruel, then you can just run rain dance and the rain dish ability if specific teams are giving you issues.
Another thing you should avoid doing is thinking that one pokemon can counter weather teams. Weather teams are made up of six pokemon, and there is no well built team in existence that will ever find itself helpless before just one pokemon. You may think that your heatran counters drought...and then it dies to a surprise venusaur earthquake and your opponent is free to sweep with volcorona. You may think that your gastrodon counters drizzle...and then you actually face a rain team and find out that this couldn't be farther from the truth. If you want to combat a weather team, one pokemon alone will not help you. Why not use the age old Celetran combo to ease your pain against both sun and rain? Hell, heatran/latias should suffice. All of the offensive chlorophyllers save for growth shiftry (whom nobody uses) are all crippled and dispatched by a healthy cresselia (who was able to stop blaziken before the ban if you don't believe me). Toxic spikes Roserade alongside Rotom-W or a scarf landorus suddenly make rain teams much easier to deal with.
To end my rambling, I should also say that we should consider tyranitar to be an anti-weather pokemon much like abomasnow. The idea of a sand team has died now that excadrill has been banned and I'm not sure if a terrakion with a 1.5 spD boost and a sand force landorus are the top threats on anybody's list. You don't need to aim to counter sand teams because there are no sand teams. There is just tyranitar, and depending on the variant, he should be losing to the abusers on said weather teams anyway (Volcorona fails to ohko specially bulky t-tar, but please try not to use that set). When used as a counter to weather, all tyranitar wver does is switch in on the revenge and then swtich out before he gets killed (unless he's scarfed). In that case, you could just use Abomasnow and take out the abuser instead of running away after changing the weather.