Driven by high-resolution NAM (North America Mesoscale) and ECMWF (European Centre for Medium-Range Weather Forecasts) atmospheric fields, an unstructured grid, cross-scale storm tide model SCHISM (Semi-implicit Cross-scale Hydroscience Integrated System Model) coupled with Wind Wave Model (WWMIII) was applied to simulate the storm tide occurred in the greater New York City during Hurricane Sandy in 2012. The 3-D barotropic, fully coupled wave-current model using ECMWF (with 12 km resolution and 3-hourly output) atmospheric forcing performs the best. The storm tide results match well with observation at all nine NOAA tidal gauges along the East Coast. The maximum total water level in New York City is accurately simulated with absolute error of amplitude less than 8 cm, and timing difference within 10 minutes. The scenarios of “NAM” versus “ECMWF”, “2-D” versus “3-D” and “with” versus “without” wind wave model were examined. Although the wave setup contributes to only 5-10% of surge elevation during the event, it clearly indicated the improvement of the accuracy for the maximum surge. Simultaneously, a high-resolution model ELCIRC-sub, utilizing the sub-grid method for imbedding high-resolution topography/bathymetry data into the traditional model grid, was developed to study the coastal inundation on land. The ELCIRC-sub contains an efficient non-linear solver to improve the accuracy and was executed on the MPI (Message Passing Interface) parallel computing platform to vastly enlarge the watershed coverage, and to expand the numbers of sub-grids allowed. Temporal comparisons with NOAA’s tidal and USGS’ rapid-deployed gauges on land showed performance with an average error of 10 cm. It accurately captured the highest surge (during Hurricane Sandy) at Kings Point both on the maximum surge height and the explosive surge profile. Spatial comparisons of the modeled peak water level at 80 high-water mark locations showed an average error less than 13 cm. The modeled maximum inundation extent also matched well with 80% of the FEMA flooding map.