The Question is this: If a character with cost 3 attacks my Sunfire, if I allow the attack to be legal, but later, before attack conlusion, I activate to stun the attacker, is that considered making the attack illegal (therefore not allowed)? Or, is it just good strategy to wait and stun after the attack is made legal?

It doesn't make the attack illegal, because it's already happened. HOWEVER, stunning an attacker or defender removes that character from the attack. So Sunfire can wait for an opponent to play a pump or three before doing his thing to both remove the attacker from the attack and getting the attacking player to waste those pumps.

It doesn't become illegal.
He is just stunned and removed from the attack. The attack resolves with no attacker and basically nothing happens (aside from the stun occurring).
As far as playing it out, as a general rule you want to play effects at the latest point possible.
So typically would want to see a 3 drop spend a pump to try and get at your 5 drop and stun it mid-combat rather than stunning it before the attack occurs.
However, it a situation where you want to prevent them from attacking (like for example if you they have an effect that triggers off attacking) you might want to just go ahead and stun them chaining off the start of the combat phase or during the build.

Thanks dudes. You guys are the champs. Dude-champs.

Another thing to think about here, if they have effects that prevent attackers from being stunned you definitely want to stun before declaring it legal or they can ruin your whole game plan.

-Battle of Wills
-oh you know that x-men physical one that makes quicksilver unstunnable when he attacks.
-Bamf
-etc.

Another good trick along these lines is attacking with a character who gives you a bonus that triggers when he attacks (Beast Boy, Commander Dylon Cir)
and then activiting your Terra/Yon-Rogg/etc. Character readies, Beast gets his +1+1, and is free to attack once more.

B.