This is how I usually try to take down a helicopter:

• If he is too far away, I usually don't even care (longer "lock-on" time, reload countermeasures, etc.)
• if he is mid to close range I usually lock-on, fire, he countermeasures
• then I fire the second shot and usually this gives me the "vehicle disabled" message

But I'm curious how you do this and if there is a more "efficient" way. For example lock-on, wait till he countermeasures, wait a bit, then fire?