I have done the flight into Zurich then taking the train from the airport to the centre of Bern many times. It is quick comfortable, reliable and punctual. Thus highly recommended.
The trip from Geneva is the same which has the added attraction of more spectacular scenery. This I have done more times in fact.
The trip through Basel is a hassle but then again only relatively so.
The travel time from airport terminal to train station in the centre of Bern is roughly equal in each case.