When you want to express that you are well capable of doing something, the usual collocation is “to be good at something”, e.g.
Some native speakers do use “to be good in” when they talk about classes at school, e.g. “he is good in science” in the meaning of “he performs well in his science class”. Others, however, consider such an expression unnatural, so you may want to avoid it altogether.
There are some idiomatic expressions where “good in” is appropriate, but these are rather rare. The most common one is “to be good in bed”:
Obviously, you cannot be good at bed, since “bed” is not an activity.