Learn English – Does “freak” have negative connotations when it’s used to describe a person’s interest in something

It usually has a negative connotation, but only a mild one. Close analogues would be words like:

• unsettling
• strange
• astounding

A sentence like this does not have any particular negative connotation: "I was thinking about asking you to bring me a cup of tea not thirty seconds ago, and here you are with one -- it's uncanny!" In this context, the "uncanny" simply indicates amazement at the coincidence.

More commonly, it's used in sentences suggesting some kind of supernatural atmosphere or occurrence. For example, "We walked in and out, and took again and again a fresh look at the uncanny stones", suggesting a ring of stones with some magical or cryptic purpose.

It would be easier to judge whether uncanny is the right word for your purpose if we knew what you plan to say.

Doesn't seem so. First of all it has another meaning

To agree with or be in harmony with

(TheFreeDictionary, near the end of page)

This meaning is obviously not negative

Returning to the meaning you had in mind. I didn't find any indication as to whether it is supposed to be always negative or not. It's nothing more than

To associate or begin to associate with

here or

Associate with, become acquainted with (especially by chance)

here From this definition fall in with implies accidental rather than negative nature of acquaintance.