Traveling interstate is no issue through CT.
Cite:
CGS Sec 29-38d. Interstate transportation of firearms through state. (a) The provisions of sections 29-35 and 29-38 shall not apply to the interstate transportation of firearms through this state in accordance with 18 USC 926A and 927, as amended from time to time, by any person who is not otherwise prohibited from shipping, transporting, receiving or possessing a firearm. Such person may transport a firearm for any lawful purpose from any place where such person may lawfully possess and carry such firearm through this state to any other place where such person may lawfully possess and carry such firearm provided such transportation is in accordance with subsection (b) of this section.
(b) During the transportation of a firearm through this state as authorized in subsection (a) of this section, such firearm shall be unloaded and neither such firearm nor any ammunition being transported shall be readily accessible or directly accessible from the passenger compartment of the vehicle. If the vehicle does not have a compartment separate from the passenger compartment, such firearm shall be unloaded and such firearm and any ammunition being transported shall be contained in a locked container other than the glove compartment or console.
(c) No person who is transporting a firearm through this state in accordance with this section may use or carry such firearm or sell, deliver or otherwise transfer such firearm while in this state.
(P.A. 99-212, S. 3.)
CarbRage - You may also want to look into getting a non-res CT Permit to Carry Pistols or Revolvers. It is effectively shall issue, nominal fee and allows you to CCW through the state. MA also issues non-resident temporary LTCs for 100 bones and good for one year.
If your M1A and AR are NY legal, chances are they are legal to possess in CT, unless the AR is a "Colt AR15" or "Colt Sporter."