In one sense, yes, you're about 2 months late. Most of the winter bees will already be either emerged or under cappings, so adding Apivar now will be no use in terms of reducing the amount of viruses they have been exposed to. If you're unlucky then the colony may fail over winter due to these viruses.
On the other hand, better now than never. It will still do some good for the uncapped larvae, and those eggs yet to be laid. And it will of course be useful in significantly reducing the overall mite population that is there over winter.
Remember though that you MUST take them out again after 6-10 weeks (depending on colony size), and this means you'll be doing this in December. You must not leave them in over winter.