No. Native English speakers would almost never use "are" in this setting. The "thing" in the boxes is undefined and therefore is a single entity rather than a number of things. Hence the plural form: "are" sounds awkward at best (even if you assume that there are multiple things in the box it still does not sound correct) and downright incorrect at worst. The word "is" is appropriate because it both covers a single item and works as a mass noun. We would understand the sentence that includes "are" but it would be another clue that you were not a native speaker.
I'm a native speaker. Yes we can use both 'is' and 'are', but it sort of depends on the person asking the question. If the questioner thinks that there is one thing in the box, then use 'is'. If there is more than the one box, I'm liable to say either 'is' or 'are'. If I use a contraction, I'll say 'what's', but will use 'what are' otherwise.