There's no single, universally agreed-upon definition of "D3 school." The NCAA Division III classification is a broad one encompassing hundreds of colleges and universities. Therefore, there isn't a readily available, definitive answer to which D3 school has the largest enrollment. Enrollment numbers fluctuate yearly as well.
To find the largest D3 school in a given year, you'd need to consult the most recent enrollment data from the NCAA or individual college websites. Even then, you'd need to carefully define what constitutes "enrollment" (full-time vs. part-time, undergraduate vs. graduate, etc.) for consistency.