First off there are not two accusatives there, das Licht is nominative.

The second one is better as others have said, the reason this is correct is that generally in German questions the word order after the initial verb is all pronouns THEN the noun subject. Sie is a pronoun and as such it goes before the noun subject. So:

Stört sie das Licht?

[lower case s for sie btw, since it is 3rd person singular] is correct.

First off there are not two accusatives there, das Licht is nominative.

The second one is better as others have said, the reason this is correct is that generally in German questions the word order after the initial verb is all pronouns THEN the noun subject. Sie is a pronoun and as such it goes before the noun subject. So:

Stört Sie das Licht?

is correct.