I can apply Vaders damage to either section of the Radier he is crew upon, correct?

Page 3 of huge ship rules:

"If a huge ship suffers damage from a source that does not explicitly affect a single section, the opposing player chooses which section suffers the damage. Crippled sections cannot be chosen. "

Agree with the above...

However, it could be debatable that the section performing the attack should be the one that recieves Vader's damage. Certainly, the rules don't say anything about this, but it seems plausible, since the attack that triggers vader originates from a explicit section (and card) of the ship.

No. Vader is definetly a source that doesn't specify a section. So the opponent chooses.

Am I the only one who sees this topic and starts humming "American Pie?"

So bye-bye to the ships that you fly,

May be Vader on the Raider or Academy TIEs,

You rolled so bad you might as well be a bye,

Singing 'This will be the round that I die....'

Personally I see it and try to work "Vader on the Raider" into a stanza with "the chalice from the palace" and/or "the flagon with the dragon".

"... but the Vader on the Raider is the crew that is true..."