Finding the lowest peak won't work reliably for estimating pitch, as this frequency is sometimes completely missing, or down in the noise floor. For better reliability, try another algorithm: autocorrelation (AMDF, ASDF lag), cepstrum (FFT log FFT), harmonic product spectrum, state space density, and variations thereof that use neural nets, genetic algorithms or decision matrices to decide between alternative pitch hypothesis (RAPT, YAAPT, et.al.).
Added:
That said, you could guess a frequency, compute the average and standard deviation of spectral magnitudes for, say, a 2-to-1 frequency range around your guess, and see if there exists a peak significantly above the average (2 sigma?). Rinse and repeat for some number of frequency guesses, and see which one, or the lowest of several, has a peak that stands out the most from the average. Use that peak.