Aiga
I didn't take a train in Estonia or Latvia yet, but in Lithuania they are pretty good, at least between bigger places and not crazy expensive. They also seem popular, and are always busy or full, so maybe it's kind of surprising that they don't get much NGO love.
On the other hand, maybe Germany just has more NGO's in general because of sheer size. 85 million people compared to about 6 million in the three Baltic States together.