Re: 5 boros fly fishing in NYC?
Please be advised that the Harlem Meer in Central Park, because of weed growth, has become unfishable most of the season. (It's okay in April and May, though.)
Your best best is probably Prospect Park in Brooklyn, and some of the lakes in Staten Island.
What has really improved is our striped bass fishing. We have a lot of new piers on the west side of Manhattan.