Contact the local Ministry of Natural Resources. Building Departments do not have jurisdiction over the water (that is what my local CBO told me). Typically if you are not increasing the size, coverage or height you can do it, adding a room above will be more effort and hoops to jump through as you mentioned- blocking neighbouring views etc. is what they are concerned with. I had to deal with them on a repair on my boat house this past summer that redid cribbing, they were very good to deal with and I did not require a permit, I had to send a plan and pictures of what it looked like and sketches of what I wanted to do. Good luck and now is the time to get started on it to be able to work next summer. Anything you do in the water has to respect spawning seasons which is typically July 15th (I believe this was the date) until October 15th.