Neighbour's dock sticks out in front of my cottage

The beds of most lakes in Ontario are owned by the Ministry of Natural Resources and Fisheries. 

The Ministry's Free Use Policy provides guidance to waterfront owners and can be found below. The policy states, with respect to Waterfront and Waterway Uses:

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Docks, breakwalls\erosion control structures with only minor backfill, single storey boathouses provided they are used strictly for private use or commercial tourism non-revenue producing purposes and are in substantial compliance with the following:

a) are mutually considered to be a necessary adjunct to the use and enjoyment of the adjoining upland property;
b) are situate directly in front of the owner’s/occupier’s dry upland parcel or a road allowance or Crown shoreline reserve abutting the dry upland parcel (generally between the projected lot lines) and do not interfere with neighbour’s use and enjoyment of their waterfront property (e.g. blocking view of lake),
c) have been approved or exempted by Canadian Coast Guard under the Navigable Waters Protection Act, if applicable,
d) in the case of a boathouse, it is used only for the storage and docking of boats. Refer to Appendix 1 for examples of multi-use structures combining free use and that which requires land use occupational authority.
e) have complied with applicable permitting requirements.
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So legally you can put a dock out in front of your property on the projection of the boundary (i.e. take the boundary line and project it out onto the water), but if it interferes with a neighbouring "use and enjoyment of their waterfront property", an issue may arise. In these circumstances MNRF may grant site specific permissions for docks to keep the peace.

I hope this helps.