I liked being able to stay in town and to be able to walk everywhere to the great local restaurants, cooking classes, markets, shops and sites.
In that vein, I recommend staying at the Anantara Resort Hoi An, formerly the Life Heritage Resort when I was there. It is a lovely hotel, with large rooms overlooking the river. It had a nice restaurant, pool and spa.
If you want to be at the beach outside of town, then the Nam Hai is for you. It is a large resort with really beautiful villas (all rooms are villas), pools, restaurants and spa, all overlooking the beach. You will have to take a cab 10 to 15 minutes into town if you want to experience Hoi An. It is now a Four Seasons resort and has been totally renovated.
For something smaller, colonial and very reasonable I would consider the Cua Dai Hotel in town. It is owned by famed chef Ms. Vy who owns four great restaurants and a cooking school in town.