Well its not like they could just pass on their findings to a news outlet, so whistle-blowing has been done very different (if at all) than it is being done today. There was however some (dangerous) mouth to mouth propaganda, with a realistic chance of getting ratted out, circulating rumours about certain atrocities and there was also some networking going on, which indeed were partially combatted by counter propaganda and through investigation and infiltration by gestapo, payed informants, sympathisants, etc.

One prominent (and iirc pretty much the one and only) example of an organization that might loosely fit into this would be the small resistance group "Weisse Rose" (the white rose), which originated from students and other intellectuals. They spreaded leaflets in which they critizised the situation, informed about crimes like euthanasia, mass murder, the moral decay, the fact that Hitler was losing the war and other consequences of the regime.

Members including Hans Scholl, Alexander Schmorell and Willi Graf directly witnessed certain crimes, like mass murder in poland or the devastating situation in the Warshaw ghetto during their 3 month service on the eastern front in 1942, which also contributed to their motivations. Between June 1942 and February 1943, the group prepared and distributed six leaflets, in which they called for the active opposition of the German people to Nazi oppression and tyranny. [1]

They started small, sending their letters via mail to other intellectuals, from which some in return started to contribute and resend the letters themselves. Since they targeted mostly intellectuals, there was at least some acceptance of their messages. Over time the group of supporters grew and they were able to spread leaflets in multiple cities in South Germany and Austria. Their sixth leaflet even reached England and it was decided to drop hundreds of thousands copies of it over Germany in 1943.[2]

Even though they seemingly often stated the obvious, it probably would qualify as "whistle-blowing", trying to inform the general population about their findings and what was really going on.

How Germany dealt with dissidents like this was straight and merciless. In case of the Weisse Rose, the siblings Scholl were being caught at the university in Munich after distributing a staple of leaflets which had been observed by a custodian. They were interrogated until first Hans, then Sophie Scholl confessed. Even though they tried to assume full responsibility, the Gestapo had enough information to identify further core members, Prof. Huber, Willi Graf, Alexander Schmorell and Christoph Probst, which all were sentenced to death. [3]

Here are the leaflets in english translation.

1 *["The White Rose", Holocaust History.org] (http://www.holocaust-history.org/short-essays/white-rose.shtml)

2 * Hornberger, Jacob G., "The White Rose: A Lesson in Dissent"

3 * Wittenstein M. D., George J., "Memories of the White Rose", 1979