I did pretty much the same as you, only my VCE landing was late at night. I spent that first night at a hotel near the airport, then took the bus and vaporetto to the tour hotel where I had a room for three nights before the tour started. I spent those days seeing everything I could that wasn't on the tour schedule -- Frari Church, San Giorgio Maggiore, Salute, Naval Museum, Correr Museum, Ca'Rezzonico, Ghetto, and lots of wandering. I bought a 3-day vaporetto pass which was a very good investment. (Sometimes it's easy to get on the vaporetto going the wrong way if you're not paying attention. That's an expensive mistake if you just bought a ticket, but a fun little adventure if you have a pass.) On one of the days I took the train to Padua and saw the Scrovegni Chapel, the Basilica, and other sights. That was an easy and worthwhile day trip. But there's plenty to see in Venice for your whole three days.
If you've been flying the night before and all day you'll be plenty tired at 6:00, but I'd say go ahead and get into the city, preferably the tour hotel if you can arrange that. Make it an early night. You'll thank yourself in the morning when you wake up in this beautiful city with time to enjoy it and get used to the clock before you start the tour. Which is a great tour, by the way.
Edit -- The previous poster mentioned taking a water taxi from VCE into Venice. That would be fast and convenient, though very expensive. There's also regular bus service from VCE to Piazzale Roma, then vaporetto to a stop that's hopefully close to the hotel. Your call, but I'd go for the bus and buy that vaporetto pass instead of spending all that money on a taxi.