Both the Blue and Red Lines will get you from the airport to the cruise terminal. The Blue Line departs every 30 minutes while the seasonal Red Line departs every hour. You have plenty of time to do this and if the weather is good it will be a nice ride across the lagoon. Both lines will stop in Murano and Lido as well as Venice before reaching the cruise terminal. The cost for a one way trip from the airport to the cruise terminal will cost 15 euro, 14 euro if purchased online before arrival.
The other option would be to take a bus or taxi from the airport to Piazzale Roma and then take the people mover to the cruise terminal. This option will be a few euro cheaper but not as scenic. The bus is 8 euro and the people mover fee is 1.5 euro.
Personally, with 5 to 6 hours before your ship departs I would take the Alilaguna water bus and enjoy the ride. It will take about an hour and 45 minutes to reach the cruise terminal from the airport. If for some reason your flight is delayed and time is tight then perhaps I would opt for the bus/taxi and people mover option.