We present a statistical method for the photometric search of rare astronomical sources based on the weighted k-Nearest Neighbors method. A metric is defined in a multidimensional color-magnitude space based only on the photometric properties of template sources and the photometric uncertainties of both templates and data, without the need to define ad hoc color and magnitude cuts which could bias the search. The metric is defined as a function of two parameters, the number of neighbors k and a threshold distance D _th that can be optimized for maximum selection efficiency and completeness. We apply the method to the search of L and T dwarfs in the Spitzer Extragalactic First Look Survey and the Boötes field of the Spitzer Shallow Survey, as well as to the search of substellar mass companions around nearby stars. With high level of completeness, we confirm the absence of late-T dwarfs detected in at least two bands in the First Look Survey, and only one in the Shallow Survey (previously discovered by Stern et al.). This result is in agreement with the expected statistics for late-T dwarfs. One L/early-T candidate is found in the First Look Survey, and three in the Shallow Surveys, currently undergoing follow-up spectroscopic verification. Finally, we discuss the potential for brown dwarf searches with this method in the Spitzer warm mission Exploration Science programs.