My wife and I arrive in Venice between 11-12 at night, and we're wondering what the best way is to get to our hotel. The hotel staff know we will be late, but we'd like to learn the quickest, cheapest options for getting there. The hotel is a quarter mile from St. Mark's Piazza.
The last Alilaguna boat departs the airport at 15 past midnight and gets to San Zaccaria at 1:37 and San Marco at 1:42. After that, you'll need to take a water taxi. The Alilaguna fare is 15 euro per person. Water taxi about 100 euro total. So Alilaguna is the cheapest (bus to Piazzale Roma stops running at 11:10 pm), and water taxi is the fastest.
I'd recommend spending the night outside of Venice. I stayed in Padua the first night (an easy bus ride), spent part of the next day exploring Padua, and then headed into Venice. And that was a very pleasant way to arrive. If you've not been to the hotel (or Venice) before, keep in mind that it can be very challenging to find a specific address during the day... I wouldn't want to try it jet lagged, late at night. And there may not be a lot of people (or open hotels) at that time of night to ask for directions. It's not something I'd contemplate. The one exception would be if your hotel is on the water and has a dock so a water taxi could take you directly there. But you mention wanting the "cheapest" way of getting there; there is nothing cheap about a water taxi, and that type of hotel is typically pricey. Also, a quarter mile from San Marco covers lots of territory. If you decide to go directly to venice, keep a good flashlight handy; Venice is surprisingly dark at night once you get away from the main squares, and you're likely to be wandering down dark, narrow pathways.
What is the name and address of your hotel? A couple things to consider: Even though there would probably be a penalty to change your flight, it might be close to the amount you would have to pay for transportation in Venice late at night, compared to much less if you could arrive at a more reasonable time. Can you change to a hotel that's closer to the Grand Canal? As mentioned above, not a terribly good idea to arrive very late in Venice.