hey hey jamesonch
i would stay in venice the whole time. your time is too short to see the places you want, spending time in train stations & on trains will take up your time getting to these places.
have you been to venice before, what is your budget in euros for the three of you, any amenities you need, mobility issues (many stairs/steps/bridges to cross with luggage on cobblestones/uneven pavement (pack light). you're in the beginning of high season to travel with higher prices, it's not only venice it's everywhere. i'd look for a hotel that has front desk help for questions, harder to find a room for 3 with the types of beds: one bed & sofa bed, three twins, family rooms. look at booking.com plus you're late booking when many rooms have been booked for months.
what time is your flight back to toronto from VCE, many are so early (6am), getting up, shower, packing, finding transportation that early depending where you're staying. we like staying in the canareggio area near train station and buses at piazzale roma, we take the more costly ride with a private water taxi. add it into our expenses with no stress,
remember check in is 2-4pm and check out is 10-11am. finding your way around can get confusing with many canals, dead ends, the fun of it. been 4 times, first time my friend and i just walked and roamed, got lost, and laughed so much trying to find our way, took a food tour, took a boat (vaporetto) to burano, an island away from venice, stayed away till late afternoon/evenings to see the sites everyone wanted to see at the same time with all the crowds.
agree with acraven about the "cruise" saying venice but trieste which is a train ride (2 hours away). since cruise ships not allowed in venice proper many are confused when they find out it's not venice, just like the cruises that stop or leave from ravenna, couple + hours to get to venice.
hurry up and book your stay and hoping all works out for you. remember where ever you decide if not venice, you will be paying train fares to get to venice and back, day tripping with all the crowds that turns people off with bad reviews. we loved staying in venice, lots to see and do.
aloha