I don't know if the time would make a difference, but to get from the airport to a hotel near San Marco you actually need to take a water taxi! When my family was there in the summer we paid around €100 for a water taxi booked in advance to carry five people and their luggage. It seems like a steep price but it was the most convenient way to make the trip -- and I would especially recommend it in your case since you'll be out at night. about 8 years ago
There is a bus you can take from the airport to Venice, and then you can take the vaparetto (water bus) to San Marco. Both cheap and very easy to do, but you will need to confirm times the bus runs (the vaparetto goes all night, just less frequently). If there is a flight coming in, most likely there will be a bus. You buy your tickets kside from a machine in the baggage claim area.
My Venice eating recs are here: http://malloryontravel.com/2011/06/cool-places/italy/non-tourist-venice-eating-for-adventure-and-enjoyment-not-sustenance-and-convenience-adventure-travel-explore-activities-photography-ecotourism-environment-adventuretourism/ (scroll down past interview).
Or there is a link on my webpage: http://TravelEater.wordpress.com about 8 years ago
The alilaguna line public boats serve Marco Polo Airport and run 24 hours a day, about once every hour. The fares are13-16 euros. They can drop you off near San Marco. It will take about 45 minutes depending on your stop. To find the boats, or the water taxis, turn left as you exit the baggage claim and follow the signs. If you decide to take a taxi, you can reserve in advance on venicewatertaxi.com. about 8 years ago