One may be good with nouns, indicating that one is proficient at use of the noun.
"Suzy is good with the cello."
"Eddy is good with a paint brush."
"Lauren is good with engines."
One may be good at a noun which is a gerund or when using the word "that" to refer to an activity.
"Patrick is good at [playing] baseball."
"Emily is good at carving pumpkins."
"Fitzgerald is good at that."
One may be good in a place--but only if the activity in question (at which one is good) is implied--or in a role (for instance, when acting).
"Jessica is good in the driver's seat."
"Derek is good in the field."
"Lesley is good in villain roles."