Switzerland's large lakes — Geneva, Lucerne, Zurich, Thun and others — are served by historic steamer and modern boat fleets, and most companies allow dogs on board on the same general terms as SBB trains: free under 30cm in a carrier, a ticket required for larger dogs.
The Day Pass Dog (CHF 25) and the monthly and yearly Dog Passes cover most lake boat operators alongside trains and postbuses, so it's rarely worth buying a separate boat-only ticket if you already have one of those.
The one consistent restriction is the onboard restaurant section: dogs are usually welcome on the open deck and general seating areas, but not welcomed into the dining section, particularly on boats running dedicated culinary cruises.