You could do the following, if you need to get to the airport that early:
Use a water taxi, it costs around 80-90 euro and the whole trip takes 25-30 minutes. Your hotel can arrange all that. – You could use land taxi from the Piazzale Roma train station. To reach Piazzale Roma you must take a night Vaporetto.
Check here for the timetable.
Check this for water bus schedules, i’m not sure they start so early.