Hi moonbeam,
There are 1 or 2 trains per hour from Milan to Venice, taking about 2.5 hours. A full-fare, 2nd class ticket is €44 per person. These trains are reservation required trains, so you will have a reserved seat when you buy your ticket. You shouldn't have any problem buying these at the airport train station in Malpensa upon arrival.
From Malpensa Airport, take the Malpensa Express Train to the Milano Centrale train station. There are 2 trains per hour, taking 52 min. costing €12. You can buy tickets at the airport train station upon arrival. Be sure to validate the Malpensa Express train ticket in a green box in the station before boarding the train or you could get a fine. You can use the Italian rail website, Trenitalia for finding train schedules and ticket prices anywhere in Italy: www.trenitalia.com/tcom-en
The station you want in Venice is the Venezia Santa Lucia station, on the island itself. All trains will stop at the Venezia Mestre station first, on the mainland, but don't get off here.
When you get off the train at the Santa Lucia station, you will be right on the Grand Canal. You can take a Vaporetti (water bus) to St. Marks Square and your hotel. Just buy a ticket at the stand near the stop. Vaporetto #1 takes about an hour.
Two of my favorite hotels near St. Marks are the Hotel Campiello - www.hcampiello.it , just East of St. Marks Square and the Hotel al Piave - www.hotelalpiave.com, just North of the square. Rick's Italy or Venice guidebooks have many more options.