With a 6' draft on our 40' sailboat, we have always sought to avoid the inlets on the Atlantic side, and just made for Montauk (our staring point is the Raritan
Bay). The sailing is off the major shipping
lanes and there are no crab/lobster traps to content with, just a few well lit fishing
We normally lay Montauk point in about 22 hours +/-, and we like to duck around the point and stay in Lake Montauk, a great place to hang out and easy anchoring
in protected waters 10' deep.
From there you have a lot of cruising opportunities:
Sag Harbor, Greenport, Cocheles Harbor, Shelter Island - Dering Harbor
Then make the rounding through Plum Gut into the sound. The first real port of call on the NY side is Mattituck, and a 5'2" draft is no problem.
of thumb is: wind
from north, stay on the CT side, wind from the south stay on the NY side.
Great spots at Port Jeff, Huntington Bay, Oyster Bay, Manhasset Bay on the NY side.
Essex, Black Rock, Mystic, Stonington, Stamford, The Thimbles, Mamorneck, Greenwich, Cos Cobb on the CT side.