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At the normal speeds of current space travel, individual atoms would not create a major problem, near light speed however, even a molecule of hydrogen would pack a bit of a punch, however, it you were able to travel near light speed, you would become very small (this is a relativistic effect that would only become significant when you are within a few percent of c) and so a much smaller target.
I expect that interstellar space would contain much more matter than intergalactic space, although it can't be very much, otherwise even the 4 light years of even a very thin gas between us and Alpha Centauri would block a huge amount of light. Matter near the central plane of our galaxy causes severe light loss to stars located in the plane and can easily amount to one or to magnitudes.
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