There are links approximately hourly throughout the day. Buy tickets at Malpensa Airport train station, not in advance, as your plane might be delayed which could render your tickets worthless.
Look at http://www.fsitaliane.it/homepage_en.html entering from 'Malpensa Aeroporto' to Riomaggiore and your 'hour' of departure, e.g. '7' for 07.00. The results will always show a change of train at M.C.LE. = Milano Centrale and at another station, e.g. Genova Brignole, Sestri Levante, la Spezia or Genova Piazza Principe (GE PP and GE PP S are simply parts of the same station).
Best end-to-end journey time is at least 4.5 hours. The three hours you have read about is the time from Milano Centrale to Monterosso, which is the only Cinque Terre train station with direct trains from Milan.
You must validate (time/date stamp) tickets for all parts of the journey for which you do not have reserved seats.