I suppose it's a silly question but I can't find a specific rule about it. There might well have been one but for whatever reason I cannot find it.

As the title asks.

Can you use a Defense Token on damage dealt by a Counter Attack?

Don't see any reason why not.

A counter attack will still follow the sequence of an attack, so your opponent will get step 2 (which he may find important) and you will get step 4. He may also like to have step 3 if say Howlrunner is around and he has swarm.

As I recall, a Counter Attack is resolved just like a normal attack but you use a number of dice as per the ability (instead of the squadron's normal dice pool). So, yes Defence tokens and anything else you can use in an attack will also apply to counter attacks.