Venice Airport

The ACTV website is being a bit sticky at this moment. My schedule on file shows an Allilaguna boat departing San Marco at 3:40 am arrive airport 4:59 am. You could short cut and pick it up at Fondementa Nova at 4:21 am. When the website gets back up, check the No 5 bus to the Airport from Piazzale Roma. The N boat runs all night on the Grand canal.

Water taxi is the best option that early if you stay in Venice proper. Still a 1 hr boat ride. 110 euros also (up to 8 people).
There is also Alilaguna that runs boats to the airport. Go to their website and see if they have a boat that can get you there at least 75 min. prior to departure (I presume it's an intra EU flight). Many opt for staying at the airport the night before an early departure because of the long and expensive boat transfer option early in the morn.

There is a Courtyard by Marriott about 1/2 mile from the airport. I think they have transportation available after 5:00 a.m. And the price is very reasonable by Venice standards. See Marriott.com

Yes, the first bus from Piazzale Roma is 4:35 am and gets to the airport at 4:56 am. If a European flight and you have your boarding pass printed, I think you'll be OK. This is cheaper than the Allilaguna and the bus drops you right at the terminal, while there is a bit of a walk from the boat dock. The N boat runs every 20 minutes in the wee hours.

You have a 6:00am flight? Usually, flights don't begin there until 6:30am. Although the airport does say that they are open 24hrs, the usual experience is that they open at 5:00am and the ticket counters open at 5:30am. You don't indicate from where in Venice you will be departing for the airport. If you were at the Hotel Papadopoli, you could walk about 800 feet to the bus. If you are near St. Marks, its about 25 minutes on the vaporetto only the regular daily vaporettos don't start running until 5:00am. But, you can take the night vaporetto. That being said, the first ACTV No 5 bus out of the Piazzale Roma is at 4:40am the last time I looked. The first AVTO bus departs at 5:00am. The usual practice from the St Marks area is to catch the 3:40am night vaporetto and make it to the Piazalle Roma well in time for the first 4:40am bus. As Roberto points out, you can take the water taxi. 90E-110E for up to 8 people. Finally, you can stay in the airport area. Courtyard by Marriott is just across from the entrance to the airport. Titian Inn and Residence is a good alternative and is also a very short distance away. FYI, our airport is the Sacramento airport. To go to Europe, Super Shuttle picks us up at 3:30am so that we can make our 6:00am flights to Chicago or Washington D.C to pick up the flights to Europe. You are not alone on this one.