Our hotel pick is Hampton Inn Helen. The rooms are large, clean, and modern. A private patio overlooks the river, the staff is friendly, the free wifi and breakfast make life easier for this families, and it's within walking distance to a number of restaurants and attractions!
If you prefer a cabin, then try the barrel cabins at Unicoi State Park for something fun, or a 2-bedroom from Georgia Mountain Rentals. Their cabins are located close to spectacular waterfalls and cabins have amazing river and mountain views.