We were in Hoi An 2 years ago in late October and stayed at the Sun River which was a bit of a hike outside of the old town.

IIRC, some thoughts from our lodging research was as follows (Open to corrections to any of our mistaken impressions):
While the old town is where we wanted to be, we didn't think we were going to get more modern lodging options right in town at a cheap rate so we were willing to trade off for a bit of distance.

We ended up booking the Sun River which was a bit of hike outside of town along the river. It was a dark walk back but we felt safe and brought headlamps. The hotel also provided bikes that you could take into town and leave a paid parking "lots" for safe keeping. Taxi rides are cheap too.

If we went again, we'd probably be open to staying on the island across from the old town if we found a suitable place. However, we haven't researched the flooding situation on the island. We did encounter heavy rain one night with some streets in the old town flooding up to my lower calf. Flooding is not a joke.

We're not really beach/resort people so staying at a place/resort along the beach north of Hoi An wasn't a preferred option for us. But we did see people biking it along the main road who we suspect were riding between beach and old town.

i'll be there in February for 3 nights and we are staying at Betel Garden Villas. it is on the outskirts of the town. it was suggested by the local travel agency that put together the private itinerary for us. Looks like a lovely, quiet place.

http://www.betelgardenhomestay.com

Last August I stayed with my family in Maison Vy, very nice small boutique hotel and if you book direct you get some nice perks