All over. Brooklyn : I would start with Gateway National Recreation areas. Gateway requires permits either to fish or park. (worth it)
(see Brooklyn and Queens pages also)
Flloyd Bennet Field, Breezy Point, Gerritson Beach. and then there is 69th street pier. Sheepshead Bay, Canarsie Pier, Red Hook. (not gateway]
Queens: Jamaica Bay
Bayside Marina, Broad Channel Beach, Cross Bay Bridge, Jetties at the entrance to fort totten in Bayside.
also Fort Tilden Park. NYC parks dept.
Gateway NRA is a 26,000 acre recreation area located in the heart of the New York metropolitan area. The park extends through three New York City boroughs and into northern New Jersey. Fishing permits are required for night time.
GATEWAY HAS NO ENTRANCE FEES. However, Beach Parking Fees are charged at Sandy Hook and Jacob Riis Park during the summer. Annual passes are available for Sandy Hook.
* Fishing Permit
$50 - Annual (recently raised)
There are fees for parking in fishing lots at all Gateway sites. Permits are available at Gateway Visitor Centers/Ranger Stations.
Public Affairs Office
(718) 354-4606 Jamaica Bay Unit
(718) 338-3799 Staten Island Unit
You can Also purchase a yearly National parkpass for $50. that allows you access to any National park that requires an entry fee. You can purchase one online at their web site. https://buy.nationalparks.org/default.asp?ref=nps