Two useful ways of thinking about the relationship between perception and critical thinking are a) separating sensation from perception and b) separating perception from other analytical skills necessary for critical thinking.

In modern neurology, psychology, and similar disciplines, sensation is the "raw data" that our eyes, ears, and other sense organs feed our brains. It is the patterns of light that strike our eyes, the vibrations that strike our ears, and so on. Perception, however, is a phenomenon that occurs within the mind. It is how we "make sense" of all of the data that we are getting from our sense organs. Not only does that not mean that perception is not always unbiased (we can perceive things differently from how they actually are, as in the case of an "optical illusion"—for example, lines drawn on a wall in such a way as to look like they should intersect when they are actually parallel or vice versa) but that there isn't necessarily any one "right" way to perceive things. One of the most famous examples of this is the "duckrabbit" (an image famously cited by the philosopher Ludwig Wittgenstein in his Philosophical Investigations). When you look at the image, you might at first think that it is a picture of a rabbit. You might also think that it is a picture of a duck. The fact is, the sensory data that you are receiving through your eyes won't tell you definitively, so your perception isn't right or wrong one way or another. This means that critical thinking involves constantly questioning our own perceptions.

Philosophically, this was an insight first proposed by rationalists like Descartes and Kant over and against empiricists like David Hume. Hume and other empiricists—the philosophers behind the natural sciences—more or less equated sense data with the truth. They believed in a universe that humans could objectively observe. This is the philosophical foundation of the scientific method. Descartes, Kant, and philosophers who followed them asked the question "What makes you think the world is the way that you think you see it?" Descartes, in his Meditations, went so far as to propose that it was possible that the whole world might actually be a set of elaborate illusions created by an "evil genius."

Kant was even more subtle. In his Critique of Pure Reason, he proposed to ask the question "what is the condition for the possibility of knowing anything about the world?" In other words, assuming that a human subject can know something about the objects around them, what conditions have to be met for this to be true? Can we think about these conditions rationally? His answer was "yes." There must be certain basic rational concepts that actually exist, apart from the subject and the object they perceive, in order for that perception to be possible. It is the job of philosophy to think critically about these concepts. This was called a "transcendental argument." These philosophers and those who followed them provided a foundation for separating out critical thinking from observation.

This brings me to my second point. Scholars in the contemporary discipline of pedagogy (the study of education) have devoted a great deal of energy to separating out critical thinking from other human activities, such as perception. The goal is to get students to move from simply perceiving the world to asking critical questions about it. A famous tool that many pedagogy scholars (and regular teachers, such as myself) use for this is called Bloom's Taxonomy. I'm including an image file for Bloom's taxonomy in this answer so you can see what it looks like. Bloom's taxonomy starts out with knowledge and comprehension. This is simply being able to accurately describe the world around you. Here we are dealing with correct perception and with the relationship between perception and sensation as I have described it above. But, once students are able to accurately perceive, remember, and describe objects in the world around them—whether that is the fizz you get from combining vinegar and baking soda or the words "Romeo, Romeo, wherefore art thou Romeo?" on the page of a book—there is still more to be done. This is where we move from perception to critical thinking, which is made up of application, analysis, synthesis, and evaluation. These are the skills necessary to form judgments about the world (e.g., "vinegar and baking soda fizz like that because of a chemical reaction"), to come up with new ideas (e.g., "maybe something else would happen if I combined different chemicals"), and to self-critically evaluate whether one is right or wrong. These are the rudiments of critical thinking.

So, to sum up, both in philosophical reflections on the relationship between sensing the world and rightly perceiving it and in the discipline of education, there is a difference between perception and critical thinking. Accurately perceiving the world is necessary for thinking critically, but it is not enough. Critical thinking starts where perception ends. Perception is getting an accurate picture of what's going on around us. Critical thinking is what we do with that picture once we've formed it.

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Critical thinking is defined as a careful type of thinking, in which the person analyzes and assesses the information put before them in a critical way. It involves coming to well-thought-out conclusions by thinking with an open mind. Thinking in this way does not have any room for biases, preconceived ideas, or incorrect data.

Human perception can have a negative impact on this process, as it can allow incorrect data into the equation. Think about if you thought you saw something, or heard someone say something, that you later discovered to have been a misunderstanding or misinterpretation. Any perceptions that you have, particularly if they are related to a subject about which you are passionate, can make you think in a biased way, rather than objectively analyzing the information that is put before you. In other words, human perceptions can be fallible in a situation in which data is infallible.

Perception can affect our critical thinking in a negative way.  Critical thinking depends on having high quality information about which to think.  If our perception gives us bad information to think about, the quality of our thinking will suffer.  We, as human beings, are very susceptible to perceiving things in wrong ways.  We can be fooled by our physical senses.  We can also perceive things in incorrect ways because we filter them through prejudices and emotions that we do not even realize that we have.  

Critical thinking depends on high quality information.  If our perception does not give us accurate information, it makes it harder for us to think effectively.