I've not done this myself, but have spoke to others that have. You are best to go thru Hell Gate. Just time the tides, make sure your motor is in good order, and have a good look out. Also plan to make sure that you have a place to harbor on the sound side of hell gate in case you time the tides wrong - City Island is likely a place to stay overnite.
Good places to stop include - Mystic, CT, Brandford, CT, Milford, Port Jefferson (NY) - alot depents upon winds, etc. Since winds are prevailing SW in the summer.....
Recommend you buy/go to library to get the appropriate cruising guides and download the NOAA coast pilot.