This is from NY DEC website: http://www.dec.ny.gov/permits/54950.html
I cut out a bunch of it to drill down to the reciprocity question.

Recreational Marine License FAQs
Frequently asked questions regarding the recreational marine fishing license:

When will the license requirements become effective?

Beginning October 1, 2009, all anglers, required to do so, must have a recreational marine fishing license.

[Note: there is pending legislation that may delay the effective date of the implementation of the recreational marine fishing license until January 1, 2010.]

Are there any reciprocal license agreements with other states where marine waters form boundaries with other states?

Yes, in certain waters, if a state grants New York recreational marine fishing license holders fishing privileges in that state's portion of the boundary water(s), then New York grants appropriately licensed anglers from that state the privilege to fish in the New York portion of the boundary water(s) without securing a New York recreational marine fishing license:

* Connecticut: those parts of Long Island Sound lying between New York and Connecticut
* New Jersey: those parts of New York Harbor, Hudson River, Kill Van Kull, Arthur Kill, Raritan Bay, and Atlantic Ocean lying between New Jersey and New York, and
* Rhode Island: those parts of Long Island Sound, Block Island Sound and the Atlantic Ocean lying between Rhode Island and New York.

Based on this, it appears that your CT Marine License would not be valid on the south shore of Long Island (Atlantic Ocean) or past the Orient Point/Fishers Island line. I'm not quite sure about New York's section of Block Island Sound.