How the eye recieves light:
1. The light rays enter the eye through the cornea (transparent front portion of eye to focus the light rays)
2. Then, light rays move through the pupil, which is surrounded by Iris to keep out extra light
3. Then, light rays move through the crystalline lens (Clear lens to further focus the light rays )
4. Then, light rays move through the vitreous humor (clear jelly like substance)
5. Then, light rays fall on the retina, which processes and converts incident light to neuron signals using special pigments in rod and cone cells.
6. These neuron signals are transmitted through the optic nerve,
7. Then, the neuron signals move through the visual pathway: Optic nerve → Optic Chiasm → Optic Tract → Optic Radiations → Cortex
8. Then, the neuron signals reach the occipital (visual) cortex and its radiations for the brain's processing.
9. The visual cortex interprets the signals as images and along with other parts of the brain, interpret the images to extract form, meaning, memory and context of the images.
This was taken from
http://en.wikipedia.org/wiki/Eye#How_we_see_an_object (I figured their source is more credible than if I just explained the same thing):
I believe the average person perceives about 50% of their environment at any given time, however, iirc from psychology class, our brain always focus' on new things that we have not yet seen. Our brain is really good at 'recreating' and filling in the rest of our memory. Our brain is constantly trying to make sense of so many new sensations that it actually creates a lot of images and fills in holes in our perception (looking out of the corner of your eye and seeing something, looking at a circle that isn't closed; your brain processes it as a closed circle). If anything, they would have filled in the 'invisible ship' with their own perception of the ship (they might not think of it as a "ship"), however, they still saw what we would describe as a huge floating wooden boat sailing towards them.
If your conjecture is true (about the native americans not being able to see a ship because they have never seen one before), then it would hold true into experiment.
EDIT: After running this simulation over in my head a few times, I have decided that the encounter would have been in this fashion:
The native americans chilling on the shore doing their native american things, then, out of the corner of either one or a few people's eye (or perhaps someone had a direct line of sight), they would notice a small obscure image. Their amygdala (the structure in your brain responsible for the fight or flight response; it analyzes all incoming physical sensory data and analyzes it's emotional significance) more than likely instantly alerted them of something odd approaching. The hypothalamus would issue an order to secrete to the pituatary gland which would issue a command to the master endocrine glands (adrenal) and the liver would then slam the body with sugar and the fight or flight response would be initiated. At this point, their brain has identified a potential survival threat and has shifted all conscious awareness to this peculiar object approaching. They would not hear the sounds of each other, the noises of nature or see anything except a huge fucking ship coming towards the shore.
They might not call it a "ship" and it's possible they could have subjectively perceived it as varying physical material objects (monster, spirit, animal, etc.), however, they SAW what we would all agree is a ship.