<em>Two heads are better than one</em> is an idiom meaning that it's easier to solve a problem or come up with an idea with the help of another person than alone.
<em>Two is company, three is a crowd </em>is an idiom usually associated with a romantic context. It's used to say that a third person should leave when two people (e.g. lovers) want to be together on their own.
So, when we compare these explanations, we can't say that these two sentences mean the same, nor the opposite.
