Greenport has some great lodging options. Our recommendations include:
Fordham House: At 817 Main, I really enjoyed this charming B&B. The room was comfortable and attractive and Halina, the owner, was so helpful in steering me to the right wineries and restaurants and helping me negotiate the ferries to Shelter Island and Sag Harbor. The breakfasts were excellent. It is a great spot from which to explore the area and the wineries. I would ask for a room towards the back, since the street along the front is somewhat busy.
Harborfront Inn at Greenport: This is a larger hotel of 35 rooms on the water and looks excellent. It is an easy walk to the ferry, to the shops and to the restaurants downtown.
North Fork Table and Inn: At 57225 Main Road, in Southold, and a short drive from Greenport, is this small inn with a wonderful restaurant. The rooms have been renovated.
The Cove Place Inn looks like a great spot on the water at 15 Bay Ave. in Aquebogue NY.