Brian, as mentioned above, there are three ways to get to the Venice-Marco Polo airport. 1) Alilaguna Blue Line (www.alilaguna.it). As mentioned above, 1st boat leaves the San Marco stop at 3:40am and arrives at the airport at 5:00am. You have plenty of time. The next Blue line departs at 4:50am and arrives at 6:09am. A bit tight.
2) The second method is to get to the Piazzale Roma. It's a major vaporetto stop. The ACTV #5 bus goes from the P. Roma to the airport. About 5E. The first bus leaves at 4:40am and arrives at 5:05am. The next one departs at 5;40am and arrives at 6:05am.
3) The water taxi. High-speed. Your hotel will arrange to have one at the hotel when you need it. Cost - 100E-115E ($155-$180 after conversion). Super OUCH!!.