What is the best way from our hotel on Lido island (across from Venice proper) to catch a very early flight
Look at the schedule for Alilaguna.com.
The earliest you can get to the airport on this water bus from Lido is 5:19AM; you need to add 15 minutes to disembark, get luggaage, and walk to check-in lobby.
I know for sure that Delta closes the check-in process one hour before departure. You may want to check with your particular airline.