Trains Prague

The tourist season is starting to pick up in May. Personally, I'd feel more comfortable booking a train unless you're flexible on your arrival date for Berlin. If you need a back-up, there are buses that run from Prague to Berlin that were pretty good, at least as of 10 years ago.
I'll let someone else recommend a site, because it's been so long since I've booked a train out of Prague.

I think you should find everything you need regarding trains running between Prague and Berlin (both directions) here, including booking sites and guidance on booking in advance:

https://www.seat61.com/international-trains/trains-from-Prague.htm#Prague-Berlin
https://www.seat61.com/trains-and-routes/berlin-to-prague-by-train.htm