In messing around with the Native civs a little, I've noticed that their ships have a key advantage over Euro warships. Namely, they fire bow-on and dont have to turn broadside. When raiding fishing boats, this is a huge help. Often fleeing fishing boats can outrun the turning ability of Caravels and Galleons so many can escape unharmed. Not so vs the Native canoes.
Also, the Native ships do a LOT of damage and they mass up well, again due to their bow-on firing aspect. Its fairly easy to have 6-7 War Canoes firing at once on a single target while getting similar 'gang up' from broadside ships is very difficult. The War Canoes do 100 points per shot(!) and can sink Caravels almost before they can even turn and get a shot off.
I realize that for balance purposes they had to GREATLY exceed the realistic naval capabilities of the real natives, but it seems that they have perhaps made a monster at least when it come to raiding fishing.