"Do you have luggage?"
"Is there any luggage?" Would be a more direct translation, out of context.
They both work, but using -が implies having rather than -は which is being.
Why is にもつをもっていますか？ not acceptable?
(In the same vein that けいたい電話をもっていますか？, or something quite similar to that, is accepted in another exercise for 'Do you have a cellphone'?)