Which method to determine population size is the least invasive

It seems that you did not provide possible answers, but the mark recapture method is one method that is not very invasive. The population size is estimated by marking a certain number of individuals and releasing them into the wild, followed by a second capture later on. The members captured the second time with the markets from the original capture are used to estimate population size in the formula s*n/x where s and n are the first and second captured population sizes and x is the number of marked inidividuals from the second capture.

You should never redesign your experiment. try and see what in your experiment you made a mistake on or try and test your experimemt with somebody else. see if they get the right results.