Well, we're about to go on our first overnight stay away from our one-year-old daughter this weekend to celebrate our 5-year anniversary. We are going to Traverse City and staying at Cherry Tree Inn & Suites. The cost seems pretty reasonable and I think it's on the water or close to it. They have refrigerators and microwaves in the rooms, an indoor pool and jacuzzi, and their website says that they have babysitting.
Since we are going sans child, I haven't researched what to do with a toddler up there. If it were me, I'd probably look into renting a small cottage on a lake that had beach front access. I'd want to BBQ, be able to have my daughter splash around in the water and play in the sand, watch movies, go out for breakfast (cheapest meal of the day to eat out). Maybe fly a kite, run through the sand dunes, look into petting zoos (I think one of the wineries has one), bring board games to play, see if there are any orchards where your daughter can pick her own berries or apples, etc. Also, you can go to the travel Michigan website to see if there are any fun festivals coming up in the area when you want to go.
The scenery in the Traverse City area (including Leelanau and Mission Peninsulas) is beautiful and it would be relaxing to soak it all in. This will be our third trip to the area.
Good luck planning your trip!