what is the best way to travel from Amsterdam to Calais by train. Also, would flying be a better option?
The best way is by train
Pick the route with one change of trains
Julie, Not sure what sort of an answer you are expecting, the best way to travel from Amsterdam by train . . . . is by train, what else can be said?
As Jazz says, just go to a good train website that covers the countries involved ( Trainline, loco2: https://loco2.com/ or DB: https://www.bahn.com/en/view/index.shtml ) and look it up.
Flying would not be a realistic option, you would have to fly to Paris or Brussels and still need a train from there.
I am curious why you want to go to Calais? It is not a major tourist location, it is a port with industry and ferries to England, plus the French end of the Channel Tunnel is outside the town.
If you want to get to England, a lot easier by train through the Channel Tunnel, which does not go via Calais.
If your reason for going to Calais is so that you can go as a ferry foot passenger to Dover - and perhaps see the White Cliffs of Dover, have you read previous threads here about that process and the disadvantages thereof? Do you know about the Seven Sisters?
Or perhaps you are hoping to get a rental car in Calais for a drive to Normandy. If so, a train to Lille from Amsterdam will be much easier and the car rental is right in the station in Lille.
I know that these are not the questions you asked, but just taking a train (or flying???) to Calais is a very unusual question.