In creative writing, you really don't need to worry about historical accuracy too much. As a matter of fact, as has been pointed out, U-Boats did indeed roam far and wide, and the mouth of the Amazon is pretty wide, so I don't see any problem with your U-Boat captain (perhaps a sensitive, thoughtful soul who only ever wanted a simple job as a fisherman but was so skilled at Naval College he kept being promoted against his will - he doesn't care much about the war but recognises that he has a duty to look after his men) steering the sub to safety, but beaching it deep in the rainforest.
You should make a great deal of the crew's initial reactions to their new environment as they emerge, blinking and nervous into the humid, steaming air of the rainforest. The chatter of exotic birds in the trees far above, the strange, unidentified noises from the greenery. The shiver of panic at the slightest glimpse of an animal. Look up animals and birds of the Amazon - it will help you with your imagery.
You're absolutely right about the beards. Fresh water on baord a U-Boat would be a vital resource and shaving was probably limited to once a week at most. Then again, how about the men start off clean shaven but start growing beards as they begin to leave their old lives behind and become more in tune with the rainforest and its ways....a metaphor for transformation and renewal?
I'm taking your "Amazons" to be the race of warrior women living in the Brazilian rainforest of the same name, rather than the Ancient Greek girls, and legend suggests that they were pretty fierce towards outsiders. I would suggest a couple of gory deaths at first - spears through windpipes as the women react in a hostile way to the Germans (but only to minor or unlikeable characters - maybe one of the men is a fanatical Nazi - he can go!) but the Amazons soon realise that they have a valuable resource at their disposal -healthy males!
Good