great job at or great job in

I see this is a controversial discussion so I accept some risk of disapproval by answering. Some account of your research (or at least your personal perception of the issue you are concerned about) would have helped to fit it to the site's purpose.

Nevertheless, I come here to enjoy my language at all levels from the simplest to the highest (where I lose competence and may only hope to learn). I wish to encourage people to use this fine site to enjoy English rather than to be discouraged by disparaging judgement or criticism, so here goes:

I find both statements to be informal and acceptable, composed in the right register for such a setting. There is no significant difference in meaning. The use of "great job", although not suitable for formal compliments, seems just right. When you say "in kindergarten" the emphasis is on what happens during the time the children are there. When you say "at kindergarten" there is little difference, apart from a hint that kindergarten is where they all go to do the great job.