Malpensa to Cinque Terre area-best transportation options

There is typically a direct IC train from Milano Centrale to Monterosso

Is this the most seamless option?

No, in my opinion it's quite the other way around. Since the Genoa - La Spezia railway runs through the 5 villages, you'd be backtracking from La Spezia to Monterosso.

Where did you find this train route? Each village has its own train station, pick one and put it as arrival station on trenitalia.com

That's terrific information, thank you. Also read we should buy tickets last minute due to unforeseen travel delays
Are you aware if there are direct train routes from Milano Centrale to Santa Margherita Ligure as well?
Thanks for the help

Marco, I did check trenitalia. Just getting my feet wet checking the train schedules. When I put in Milano Centrale to Vernazza, that is the route that was offered. Did seem silly to bypass CT and go to La Spezia to backtrack, agreed. Too many transfers after a long day of flying!

Am also looking at transportation Milano Centrale to Santa Margherita Ligure and how seamless it is to stay in SML and go back and forth to CT; changing trains or limited trains after a certain hour

I do not see amy direct train trains from Milano Centale beyond Genoa in early September. You will have to change there at either Piazza Principe or Brignole.

I believe you would have to change in Rapallo to reach SML

It’s too early for September
Wait til all schedules are updated first week or so in June

Go to:
www.trenitalia.com
Select English if needed
Enter:
from MALPENSA AEROPORTO T1
to NAME OF VILLAGE*
Enter a date in the next week or so. (The September timetable is not downloaded until June, but it won’t change much and you can see your option)

*Cinque Terre means 5 lands. As the name suggests there are 5 villages you can choose from, and all have a train station (in order of appearance coming from Milan)
MONTEROSSO
VERNAZZA
CORNIGLIA
MANAROLA
RIOMAGGIORE

Monterosso is the largest and most important station, so it is the only one where some InterCity (IC) trains stop. All others have only Regional (slower) trains. Some IC trains from Milano Centrale go to Monterosso without requiring to change trains.