First off, a quick note on NAIP: Unless something has changed recently, NAIP imagery is visual 8-bit data that is not suitable for calculating radiometric indices from.  The 8-bit NAIP values will have been scaled differently for each band, so there’s no meaning to NDWI or NDVI calculated from an 8-bit visual 4-band product.  If you're working with 8-bit NAIP data, then any NDWI/etc values that are being calculated cannot be correct and can only be used in a relative manner (e.g. comparing different parts of the same image).  The absolute values themselves will have no meaning.

However, if there are NAIP products that are radiometrically calibrated and not 8-bit visual, then disregard that.

With that said, NDWI when caculated from the green + NIR bands (as opposed to using SWIR wavelengths) is not a reliable indicator of water.  Muddy water or water with algae will very commonly have negative NDWI values.  Shallow water will also frequently have negative NDWI values.  Only very clear and deep water would be expected to have a positive NDWI.  Water with mud or algae will reflect more energy in NIR than in green.  Clear water adsorbs NIR wavelengths, but muddy water is often quite reflective in NIR, as are algae blooms.

NDWI made with NIR instead of SWIR can still be useful for classifying water, just not when it’s used as an absolute threshold. Instead of applying a constant threshold, look for a bimodal histogram and separate the two modes.  Otsu thresholding is the most common approach for that.  Otsu thresholding of NIR-based NDWI is often a good method of classifying water.  Absolute value threshold won't work for NIR-based NDWI except for very clear and deep water, however.