Time between arrival at Malpensa and catching train to Varenna

It doesn't generally take long to go through customs, there is no customs line, you just walk through the "nothing to declare gate". At most you get stopped by a customs agent (gray uniform) who might ask you where you are flying from and maybe pick you for a bag search. But it's extremely rare, I've never been picked in 30-35 times flying to Italy.
You will have gone through passport control (immigration) in Frankfurt, when you entered the Schengen zone, so that is already taken care of. The flight from FRA to MXP is really like a domestic flight within the US.
The travel time from MXP to Milano Centrale is about 50 min.
The question is whether:
1. your flight is on time
2. how long you have to wait for the next train to Milano Centrale (generally one every 30 min)
3. How long you have to wait for the next train (to Genoa then La Spezia) from Milano C.

If your intention is to buy tickets in advance, be aware that discounted tickets purchased in advance are not refundable if you miss the train. You can always buy full fare (BASE) tickets at the Malpensa station, they don't run out of those. I wouldn't risk buying discounted tickets for the day of arrival. It's very hard to predict whether a flight is on time or not. You might miss your connection at FRA and have to take the next flight to MXP. That happens a lot with intercontinental flights.

Allow about 30 minutes after getting off the plane. You will have been through immigrations in Frankfurt and customs is a walk through the door - Nothing to Declare. The trains runs ever 30 minutes so you will most likely have some wait time and 45 mins on the train to Centrale.

PS Posting at the same time as Roberto. Small clarification on tickets - all tickets are non-refundable IF you miss the train. The cheapest discount ticket is never refundable. The other two classes of ticket are exchangeable if exchange is make prior to the train's departure.

Oops Roberto, I think the OP is looking for Varenna-Esino. I too get it mixed up with Vernazza all the time.
Trains to Varenna-Esino leave Milano Centrale at 14:20, 16:20, 17:20, 18:20, 19:20, 20:20. The 18:20 train requires a connection at Lecco, so it takes about 1 1/2 hours. The other trains are direct and take a little over an hour. Since these are regional trains and only cost 6.45 euro, just buy a ticket at the station (you may even be able to buy it at the MXP station), and as Ken says, DON'T FORGET TO VALIDATE IT BEFORE BOARDING.
I get the terminus of the Bernina Express mixed up with the capital of Albania.

Oooops. Freudian Lapsus.
Yes Varenna is on the Lago di Como, not at the Cinque Terre.
Well, still you need to go to Milano Centrale.

Chris,

Actually, the timing is not a huge problem. You'll likely be arriving at MXP Terminal 1 and regardless of how long it takes you to deplane and get to the rail station, there are frequent departures so it won't take long to get to Milano Centrale.

When you arrive at the airport rail station, buy your tickets direct to Varenna-Esino. They will likely provide you with two cards (tickets). Take the Malpensa Express to Milano Centrale. One important point to note is that they operate two routes, one to Centrale and one to Cadorna, so BE SURE to board the correct train. DON'T forget to validate!

When you arrive at Milano Centrale, you'll likely have a short wait until your train to Varenna departs. As I recall, there are departures about every two hours. You might want to take a printout of the schedules so that you can use one of the direct trains, rather than one that has a change. If you need to use the WC at the station, you'll need to have some change on hand, as it's a "pay" facility. Watch your luggage and be vigilant for scammers! One other point to note is that they sometimes don't display the Binario (Track No.) of departing trains until 20-30 minutes prior to departure, so keep watch on the electronic board. Prior to boarding the train to Varenna, BE SURE to validate!

The trip to Varenna will be 1H:03M if you use a direct train. At about the one hour mark, get your kit together and prepare to disembark promptly, as they only stop for about a minute. You should be able to walk to your hotel, as most are downhill from the station, but there may be a Taxi waiting at the station.

One final point - you may want to buy the tickets for your outgoing journey from Varenna in Milan, as the ticket purchasing options at Varenna are a bit "limited". There is a local travel agency in town that sells rail tickets, so you could also use their services.

Happy travels!

Thanks to all for your information and advice! It's helpful to be blue to rely on those who have experience!

Sorry! I need to proof more carefully!
It's helpful to be able to rely on those who have experience!