It's very good to remember that LeBlanc's silence takes a bit of time to set up; she has to hit her Q, wait for the projectile to hit (which isn't very long, but she can't just QW, there's a pause), and then use a second spell to actually get the silence.
Note that she can use her Q and then wait a couple of seconds to start the combo, but the silence proc is only six seconds, so she must be fast.
Your average LeBlanc character is very predictable, and does things the exact same way every time. Keep that in mind and try to predict her movement. Prediction is a huge part of the game, and all the good players can tell when another has made a mistake.
Those two reasons are why she is unlikely to be picked in high elo except as a "counter" to APs who do not have CC.
That being said, some good counters:
- Fiddlesticks counters LeBlanc all day. Instant fear beats half-second (one third if you're good) silences.
- Anivia and Morgana do well against LeBlanc, as both can survive the burst, and both outfarm LeBlanc to no end. LeBlanc needs lane control.
- LB's range is actually a bit underwhelming, slightly compensated by her W.
That being said, Ezreal and Kog Maw (if the meta ever returns to them being AP) do well against LB.
- Kassadin > LB (one skill silence)
- Mordekaiser wins due to tankiness and lane control
Point being, LeBlanc actually loses to quite a lot, which is why she isn't picked as the first AP. She's picked against people she can go 12-0 with in the laning phase.