We are taking the 6:43 AM train to Rome from Venice. How long will it take to get to the train station from San Marco by Vaporette?
It should take about 40-45 minutes. however, like most public transport, it's not how long it takes but when the transport leaves to get you there in time. It appears that depending on how early you want to get to the station and which San Marco vaporetto stop you can get on at, you will need to catch a vaporetto around 04:30 to 05:30.
www.actv.it has the schedule
Allow at least 1-1/2 hours; 2 hours is better. It takes longer than you think. You will want to check the vaporetto schedule to see if they run that early. I barely made an early morning train last spring because I didn't allow enough time.