Depends on what you see as malignant. Write up a list of things you would not want in a program and use that as a guideline. For example, some may say a program is "malignant" because they give a lot of intern responsibility. This is why programs like Hopkins or MGH are considered "malignant" by many applicants. Others may say the same thing because a program holds the hand of their interns on average more than other programs. Personally, I would hate this and ranked programs lower for this reason. I know this is most likely a minority opinion.
The only true malignant environment that I know of is the New York City residency system with the lack of resident unions to counter the very strong nursing unions. The lack of unions makes interns take on a majority of true scut work (bringing patients down to radiology themselves, doing your own lab draws etc). Even so, some programs like Mount Sinai are exceptionally supportive and a friendly environment to train. You really need to make sure other programs have similar support in this city, otherwise, I would avoid training in NYC as a resident and come back as an attending/fellow.
Less malignant in my eyes is more about some combination of support (from fellow residents and program leadership) and self worth that your training is preparing you well for the future. Some programs may push their residents to work hard, but the residents are happy because they are getting excellent training for their future career. Others hate their program, even when light on hours, because the attending and senior residents just do not want to teach or provide no support.
There is no good tool. The only way you can judge these is to apply, meet the residents to see if you are similar to your personality. I would also watch the mannerisms of how residents explained why they liked their program. Almost everyone I met on the interview trail "loved" their program. Probably 50% had body language that matched their words. There will be at least 1 or 2 programs you rank low (or not at all) due to this vibe.
Hope this helps.