Screw Hatteras, stay in Ocracoke. No specific recommendations on where to stay. Season is over, so the rates should be good. Try VRBO.com, or stay in one of the BandB's in the village. If its not in the village, don't bother.
http://www.bedandbreakfast.com/ocracoke-north-carolina.html You're just coming out of the tourist season, alot of stuff might be battened down. Weather will be iffy in a month. Should be mild, but it might be blowing, and when it's blowing its got a serious bite. But there won't be any crowds. Just be prepared for cold fall weather, with some long pants and rain jackets.
Like Chris said, make the trip up to the memorial. Check out the lighthouses. You can Pretty much do the whole run to the Currituck light and see the memorial in one day from Ocracoke or Hatteras.
Eat local, don't bother with anything that looks like a chain. Try some "downeast" pig BBQ. Crabs of course.
Sit in an adirondack chair and watch the sun come up over the Atlantic with a hot cup of joe. This is the best time of the year for beach combing, too.
Enjoy!