We are a couple traveling to Varenna the beginning of Sept looking for a nice, but reasonable accommodation for 2 nites.
We stayed at the Orange House, a two room B&B located between the train station and the ferry. It is very reasonably priced, clean and comfortable, and the owners are wonderful.
We have stayed at the Villa Cipressi and really enjoyed ourselves at a reasonable price. http://www.hotelvillacipressi.it/en/index.html