Finally got a copy of the public act. NOTE - as of 10:36am on 6/16/09, I do not know if the Governor has signed the bill. Therefore, at this time this is for informational purposes. The public act is 09-173, it has other items besides the marine fishing license in it, but for the sake of brevity I redacted the other portions of the bill. I bolded areas that pertain to some of the questions you have been asking.

House Bill No. 5875
Public Act No. 09-173
AN ACT AUTHORIZING SPECIAL DISTRICTS TO MAINTAIN WATER QUALITY IN LAKES, STATE LAND WHERE HUNTING IS PERMITTED, THE ESTABLISHMENT OF A MARINE WATERS FISHING LICENSE AND THE TAKING OF SHELLFISH IN WESTPORT.
Be it enacted by the Senate and House of Representatives in General Assembly convened:

Sec. 4. (NEW) (Effective June 15, 2009) (a) Except as provided in subsections (b), (d), (e) or (f) of this section and other provisions of chapter 490 of the general statutes providing specific license exemption, no person more than sixteen years of age shall take, attempt to take or assist in taking any fish or bait species in the marine district by any method or land marine fish and bait species in the state regardless of where such marine fish or bait species are taken, without first having obtained a marine waters fishing license as provided in section 5 of this act.
(b) No marine waters fishing license shall be required for any person who is rowing a boat or operating the motor of a boat from which other persons are taking or attempting to take fish.
(c) The taking of fish and bait species as herein provided shall be regarded as sport fishing and the taking or landing of such species in the marine district by commercial methods for commercial purposes shall be governed by other provisions of chapter 490 of the general statutes.
(d) No marine waters fishing license shall be required for any resident of the state who is participating in a fishing derby authorized in writing by the Commissioner of Environmental Protection provided
(1) no fees are charged for such derby, (2) such derby has a duration of one day or less, and (3) such derby is sponsored by a nonprofit civic service organization. Such organization shall be limited to one derby in any calendar year.
(e) No marine waters fishing license shall be required for any person who is fishing as a passenger on a party boat, charter boat or head boat registered under section 26-142a of the general statutes and operating solely in the marine district.
(f) The Commissioner of Environmental Protection may designate one day in each calendar year when no license shall be required for sport fishing in the marine district.

Sec. 5. (NEW) (Effective June 15, 2009) (a) Except as provided in subsection (b) of this section, the fee for a resident marine waters fishing license shall be ten dollars and the fee for a nonresident marine waters fishing license shall be fifteen dollars. Persons sixty-five years of age and over who have been residents of this state for not less than one year may be issued an annual marine waters fishing license without fee. The town clerk shall retain a recording fee of one dollar for each marine waters fishing license issued by him or her.
(b) Any nonresident residing in one of the New England states or the state of New York may procure a marine waters fishing license for the same fee or fees as a resident of this state if he or she is a resident of House Bill No. 5875 a state the laws of which allow the same privilege to residents of this state.

Sec. 6. Section 26-46 of the general statutes is repealed and the following is substituted in lieu thereof (Effective June 15, 2009):
(a)If and when the state of New York, the state of Massachusetts or the state of Rhode Island enacts a similar law granting reciprocal privileges to residents of this state, any person who holds a license to fish in inland waters in the state of New York, the state of Massachusetts or the state of Rhode Island may fish in inland waters lying partly in this state and partly in such adjoining state, or in such waters as negotiated by the Commissioner of Environmental Protection of this state and any similar authority in such adjoining state, without a nonresident inland waters license to fish as required by this chapter, [;] provided such nonresidents shall be subject to all other provisions of the statutes and the regulations of the commissioner relating to fishing in lakes and ponds.
(b) If and when the state of New York, the state of Massachusetts, the state of New Hampshire, the state of Maine or the state of Rhode Island enacts a similar law granting reciprocal privileges to residents of this state, any nonresident who holds a marine waters fishing license issued by one of said states having such reciprocal privileges may fish in the marine district or land marine species in Connecticut and shall not be required to purchase a Connecticut nonresident marine waters fishing license. Such nonresidents shall be subject to all other provisions of the statutes and the regulations of the commissioner relating to fishing in the marine district.

Sec. 7. Section 26-15 of the general statutes is repealed and the following is substituted in lieu thereof (Effective from passage):
The state of Connecticut assents to the provisions of the Act of Congress entitled "An Act to Provide that the United States Shall Aid the States in Wildlife Restoration Projects, and for Other Purposes", approved September 2, 1937, and the Commissioner of Environmental Protection is authorized and directed to perform such acts as may be necessary to the establishment and operation of cooperative wildlife restoration projects, as defined in said act of congress, in compliance with said act and with rules and regulations promulgated by the Secretary of the Interior thereunder, and no funds accruing to the state from license fees paid by hunters, including, but not limited to, license fees paid by hunters pursuant to section 26-28 shall be diverted for any other purpose than the protection, propagation, preservation and investigation of fish and game and administration of the functions of the department relating thereto.

Sec. 8. Section 26-14 of the general statutes is repealed and the following is substituted in lieu thereof (Effective from passage):
The state hereby assents to the provisions of Public Law 681, 81st Congress, entitled "An Act to Provide that the United States Shall Aid the States in Fish Restoration and Management Projects, and for Other Purposes", approved August 9, 1950, and the Commissioner of Environmental Protection is directed to perform such acts as may be necessary to the conduct and establishment of cooperative fish restoration projects, as defined in said act, in compliance with said act and rules and regulations promulgated by the Secretary of the Interior thereunder; and no funds accruing to the state from license fees paid by fishermen, including, but not limited to, license fees paid by fishermen pursuant to section 5 of this act, shall be diverted for any other purpose than the protection, propagation, preservation and investigation of fish and game and administration of the functions of the department relating thereto.

This is just plan awsome. I dont knwo why they didnt Iron this all out with the states last year. Classic plan classic. Just because I am un sure about coming back from tuna fishing I am going to get a licence in all three state then that way I will have alot of trouble.

This is why we need a federal licence and the hell with all the states.

I don't know what letter you are talking about from New York. But, if you are fishing in NY waters, you need to comply with NY laws. I don't know if NY recognizes a CT charter license in their waters, I wouldn't think they would.