Hi there!
All three of these are grammatically correct, and the first two are both used in natural spoken english. The third (I think it to be funny) seems a bit strange to my American English ears.
1. I think it funny. This is usually followed by "that..." For example, "I think it funny that no one seems to like cookies, yet that's all anyone brings to share." (I don't think this would ever happen, only because cookies are wonderful.). In essence, this phrase means that you find something about the world strange, but not necessarily actually funny.
2. I think it's funny. This means that you think that "it" whatever "it" is to be actually funny.
These are very subtle differences, and may be variable across different dialects/accents of English. So you know, I am a native American English speaker from Southern California, I am 22 years old, and college-educated.