You can fly Kenmore Air from Seattle to Vancouver (or Victoria for that matter) if floatplanes tickle your fancy.
The COHO Ferry runs from Seattle to Victoria as does the aforementioned Victoria Clipper plus there's the small Anacortes Ferry that runs between Anacortes Island WA and Sidney BC, just north of Victoria on the Saanich Peninsula.
BC Ferries operates between Victoria (Swartz Bay, north end of Saanich Peninsula) and Vancouver (Tsawwassen, south of Vancouver) but there are no options to take a boat from downtown to downtown so you'd need a car (or take the BC Ferries bus).
Harbour Air and Helijet are options if you want to go Victoria to Vancouver too.
Really though, Victoria is Canada's nicest city so I'd just visit there and forget about the logistics of trying to get to the lower mainland.
