Malpensa to Bergamo

Probably the most inexpensive:
http://www.orioshuttle.com/_eng/

Select the bus line 3 from the above.

Best I don’t know. It depends on what is best for you. If best means fastest, then a taxi is best.

I just take the train from Malpensa to Bergamo with a connection through Milano Centrale.

EDIT: Thanks, Roberto for pointing out the different train station. I took the route through Milano Centrale which probably took more time.

If you decide to take the train option as suggested by Jean, maybe because the bus schedule doesn’t fit your needs, the station where you change trains is MILANO PORTA GARIBALDI.
The cost of the train is €18 and the journey time from the airport to Bergamo is about two hours. Once at the Bergamo station however you need to take the ATB city bus to the airport, which departs every 20 minutes and takes about 15-20 min to reach the airport. The cost of the ATB bus is puny (less than €2). You could also take a taxi but it would cost you about €15-€20.

Thanks for all the suggestions!

I found that www.Flixbus.com also has direct buses (no transfers) from Malpensa to Orio al Serio airport for €22 one way.

Of course if you are willing to transfer at Milano Central station, besides the train option or the train+bus option there are many options. For example www.autostradale.it buses have plenty of buses from both airports to the Csntral station. The bus company www.terravision.eu also has the same.