My husband and I honeymooned in Door County and we stayed at the Wave Point Inn marina is Sturgeon Bay. It was FANTASTIC!!! We had two fireplaces, private balcony facing the water (on the bay side), breakfast delivered to our door each morning, a hot tub, everything...full kitchen, etc. The rooms are very reasonable! The only downfall was its location, which is set aside about 10 miles or so from the city I believe. I know it was a decent drive to get there for anything else but totally worth it.
Wavepointe Marina & Resort
We are getting ready to vacation up in Door County with my family. Funny how I used to live just south of there but now I'm vacationing there!!! I recommend since you still have some time to go on the Door County Chamber of Commerce web site and sign up to receive their free Door Couty Tourist Guide magazine. Lots of great suggestions in there for places to stay. We just booked a stay at the Scadinavian Lodge which is not on the water but looks like a fantastic place to stay with kids.