NY is a massive state with thousands of wild trout streams and ponds.  There is no single, reliable data source which covers the whole state.  It is possible, however, to put together a pretty good  idea of where to look for wild trout.

Probably the two best resources are the EBTJV dataset (illustrated here), and the "Water Quality" dataset which, while incomplete, is a great complement to the basin data.  Be sure to check out the varied resources we've collected about NY State, which are accessible from the "NY Resources" menu in the sidebar.

Source: Eastern Brook Trout Joint Venture, Google Earth

The photo above shows the brook trout habitat dataset published by the Eastern Brook Trout Joint Venture, displayed in Google Earth.  You can download the complete dataset in KMZ form, which can be used in Google Earth.  If you don't use Google Earth (a decision you may wish to reconsider), you can download a detailed map based on an earlier version of this dataset.  Both are available in the "NY Resources" menu in the sidebar.  The color coding in the photo is as follows (from best to worst)...

• Blue
  

• Green
  

• Yellow
  

• Orange

• Red
  

Keep in mind that brook trout can be diminished by other trout species, so some red areas may be excellent wild brown or rainbow water.  But it's almost certain that the yellow and better areas are great places to find wild trout.  Areas not surrounded by a colored line don't hold brook trout at all, though migh hold other species which are more tolerant of warmer water (see species distribution maps).

Note: these data are coded by drainage.  Not every stream within a drainage will hold trout, though the majority will, especially within the better habitat.