If my opponent has a creature with extort out, then casts a spell that I counter, can he still pay the 1 mana to trigger extort?
Yes.
According to the Gatecrash FAQ here's the official rules for extort:
702.100. Extort
702.100a Extort is a triggered ability. "Extort" means "Whenever you cast a spell, you may pay . If you do, each opponent loses 1 life and you gain life equal to the total life lost this way."
So Extort is a triggered ability that is added to the stack when a spell is cast. Triggered abilities are added to the stack before priority is passed.
Does he have to choose whether to spend the mana before or after I have countered the spell?
The Gatecrash FAQ clarifies when the mana is paid:
You may pay {W/B} a maximum of one time for each extort triggered ability. You decide whether to pay when the ability resolves.
If the counterspell is added to the stack after the triggered ability, it will resolve first. The player whose spell is countered gets to choose whether or not to pay the extort after the counterspell resolves. Of course, this has implications if the counterspell was something like Spell Rupture.
However, as @AlexP rightly points out, the smart counterspell caster will wait for the extort trigger to resolve, and see whether their opponent decides to pay the mana for it, then decide whether or not to cast a counterspell like Spell Rupture when they receive priority.