You passed Physics + Chemistry + Math (PCM) but your chemistry marks are low.

You are saying that if Biology is considered instead of Chemistry , you fall under the top 20 percentile of your board.

Biology can be considered as the third subject (instead of Chemistry) only if it was a part of your official 12th board subject combination or mentioned in your marksheet.

If your official 12th marksheet includes Physics, Mathematics, and Biology as subjects , and your percentile is in the top 20% of your board based on Physics + Math + Biology , then yes, you are eligible for admission to NITs through JEE Main.
However, if Biology was not part of your original subject combination (i.e., you didn’t actually study or take Biology in your board exams), then you cannot replace Chemistry with Biology just for percentile calculation.