I would opt for either a taxi or the bus to get from the airport to Piazzale Roma. There are two bus companies, ACTV (public transport) and ATVO, which both provide service from the airport to Piazzale Roma. The buses run until 1 am so you should be okay. A taxi is also a good option at that hour and will run 40 euro plus tip. Piazzale Roma is the end of the line for land transportation, and from here you can take the Vaporetto and get off at the San Marco terminal. The Vaporetto will still be running at that hour.
There is a service called Alilaguna that runs water boats directly from the airport to Venice, but at your arrival time you may wind up waiting 30 minutes for the next boat. You can try a private water taxi but keep in mind that they are very expensive. I think the bus/taxi followed by the Vaporetto will be your best option.