The Ha An Hotel right in the old town of Hoi An comes highly recommended. We stayed here some years ago but well run when we did. http://journals.worldnomads.com/simon_monk/post/455.aspx
This is their web site http://www.haanhotel.com so you can contact them directly. over 9 years ago
You can try Thanh Binh 3 hotel in center. There a lots of hostel in Hoian center where you can easily walk down to town shortly. Good hostel vary from 15-30$ breakfast incl.
You can contact directly to them or contact us www.tamsingh.com for more info.
Good luck, about 7 years ago