The Hotel Fremont on the Wolf River is a nice place I can personally vouch for. You have several lakes, all connected, to boat around to, I have plans with the neighbors up north to take a trip on the Fox River nearby, through the locks.
In Oshkosh, near Team Winnebagoland where a number of folks have bought their boats, there's the Best Western in Oshkosh on the waterfront. Depending on the time of year, there's the ampitheater really close by that you can boat right up to, there's the EAA that can be gotten to nearby - not on the water, but close enough to consider visiting around that time of year.
Here's the chain that is near my place up north - starting with Partridge Lake, connects via the Wolf River to Lake Poygan (the lake I'm on). Poygan connects to Lake Winnecone, then Lake Butte des Morts (Oshkosh) and Lake Winnebago. If you're up for camping, Calumet County Park is right on Winnebago, but that's for when you run out of hotel perks
Lastly, I dunno if your hotel perks will work for this, but I'm considering trying to hit Mackinac Island with the boat. It looks crazy fun to me, but it might just be outside your travel limit.