Our direct perception of reality through our senses is entirely dictated by our biology. Take for example the fact that we can see colours and hear sounds. Our brains represent different wavelengths of electromagnetic radiation as colours, but the wavelengths themselves do not have "colour". Similar, our brains represent different wavelengths of vibration as sound. Without our biological input and interpretation mechanisms, neither colour or sound exist. Additionally, we can only perceive and interpret very narrow ranges of these phenomena. We can only see electromagnetic waves in the range of 400-800 nm, which is why we can't see gamma rays, radio waves or other parts of the spectrum. Similarly, we can only hear certain frequencies of vibrations.
What is unique about humans (at least on earth) is that we have devised methods for us to extend our knowledge beyond our senses by the use of sophisticated tools and logical reasoning.
I also think it might be valid to consider that there is a difference between knowledge and intelligence. Again, our biology may limit our ability to acquire knowledge, but this is not the same thing as it limiting our intelligence. Dolphins, some primates and even some species of cephalopod all exhibit signs of intelligence (and consciousness as well, which may be more important than intelligence), but their biology does not allow them to interact with the world in the way that we do.
Where does this leave us?
For your first question:
..isn't it reasonable to assume there are not just more intelligent species out there, but species or entities who operate on an intelligence tier completely beyond our reach and who we may not even be able to converse with?
I think it is reasonable. However, our ability to converse or interact with them may not be a sign of our relative intelligence levels. If some alien species (or our far future descendants) survives Fermi's "Great Filter", then they will have potentially millions of years of an evolutionary head start on us, and will likely be far more intelligent than we are. Frankly, any Artificial General Intelligence that we create will rapidly become far more intelligent than we are.
And to your second question:
...is our biology limiting us from knowing everything?
This depends on how we define "knowing". My biology prevents me from "knowing" what an electron is "like" in the sense that I "know" about cats (for example). However, I can use the tools that my biology has allowed me to develop to describe how an electron behaves in certain circumstances.