data = {'Site 1': '31.336968, -109.560959',
        'Site 2': '31.347745, -108.229963',
        'Site 3': '32.277621, -107.734724',
        'Site 4': '31.655494, -106.420484',
        'Site 5': '30.295053, -104.014528'}

import geopandas as gpd
from shapely.geometry import Point
gdf_locations = gpd.read_file('/Users/admin/Downloads/tl_2016_us_zcta510/tl_2016_us_zcta510.shp')

[Longitude]    [Latitude]
x = np.array((-73.986946106, 40.284328461))
x_pnt = Point(x)
filter = gdf_locations['geometry'].contains(x_pnt)
print(gdf_locations.loc[filter, 'GEOID10'])