I have some large netCDF files that contain 6 hourly data for the earth at 0.5 degree resolution.
There are 360 latitude points, 720 longitude points, and 1420 time
Not sure if you have considered cdo to extract the point ?
cdo remapnn,lon=x/lat=y in.nc point.nc
Sometimes CDO runs out of memory, if this happens, you might need to loop over the yearly files, and then cat the separate point files with
cdo mergetime point_${yyyy}.nc point_series.nc