A vaccuume cleaner does a good job sucking the beasties up, but it will not erradicate them. I suggest you treat every trap in your house, keeping them closed, or covered with a bit of bleach water 24/7 for 2 weeks, and see if that eliminates the problem.
I did a little research on the little beasties. It takes about 10 days minimum at ideal temperatures to complete a life cycle. At colder temps, it will take longer. So, you will have to eliminate ALL areas where they could have access to a moist and nourishing environment for a few days past their life cycle in order to eliminate them. If they are getting in through a window screen, that's a whole other matter, but I suspect, they have found a breeding ground in your house, and I suspect your drain traps.
Life cycle of Drosophila
The drosophila egg is about half a millimeter long. It takes about one day after fertilisation for the embryo to develop and hatch into a worm-like larva. The larva eats and grows continuously, moulting one day, two days, and four days after hatching (first, second and third instars). After two days as a third instar larva, it moults one more time to form an immobile pupa. Over the next four days, the body is completely remodelled to give the adult winged form, which then hatches from the pupal case and is fertile within about 12 hours. (timing is for 25°C; at 18°, development takes twice as long.)