The three cheapest bus companies providing connections between Amsterdam and Prague are StudentAgency, Flixbus and Eurolines.
StudentAgency will typically cost around 39 euros, but will be more expensive as seats are booked and can be cheaper when there are sales (which are quite common, I have traveled similar distances for them for 19 euros).
Flixbus will typically cost 39 euros as well, though in my experience the cheapest tickets are harder to come by and 49 is somewhat more typical.
Eurolines has the worst buses out of the three companies, but prices start at 33 euros typically. Personally I prefer paying the premium for StudentAgency (or alternatively Flixbus).
In general plane tickets aren't even that much more expensive, but you need to book them far earlier. Both bus and plane tickets increase in price the later you book, but plane tickets increase in price significantly more.
EasyJet flies between Amsterdam and Prague starting with prices of 48 euros.
Czech Airlines also flies this connection, but will typically cost at least 10 euros more.
Train travel I am a whole lot less experienced with, but in general it's more expensive than bus travel, with the advantage that it's fast and can be booked relatively late for relatively stable prices. Whilst plane tickets will cost 3 or 4 times as much last minute as they did when booked early, with train travel the price might have increased less than 1 time. As far as I know train tickets will clock in around 100 euros.