Greenport Harbor is no longer the great fishing and whaling center, but it is still a popular destination for boaters seeking quick access to the Atlantic Ocean. There are several wharves in Greenport Harbor.

The State of New York owns, and the Village of Greenport operates the Greenport Harbor Commercial Fish Dock to moor commercial fishing vessels and receive fish. The dock is served by one surface track that connects with the Long Island Railroad. With three berths with alongside depth of 4.9 meters (16 feet), the Greenport Harbor Commercial Fishing Dock has one berth that is 30.5 meters (100 feet) long and two berths that are 97.5 meters (320 feet) long.

Alice's Fish Market at Greenport Seafood Dock Company owns and operates their own dock in Greenport Harbor to receive fish and seafood. A concrete building on the north side of the platform is used to process fish and sailfish bound for retail markets. The dock has alongside depth of 3.7 meters (12 feet) and three berthing spaces of 21, 14, and 9.1 meters (69, 46, and 30 feet).

Robert T. Cooper Inc. owns and operates the Seafood Dock in Greenport Harbor to receive fish, ice fishing boats, and fuel and moor company-owned vessels. A pipeline links the wharf to two underground storage tanks with total capacity for 95 barrels of diesel fuel. There is also a fish-processing building at the rear of the dock. The Greenport Harbor Seafood Dock has three berthing stations. One has berthing distance of 35.1 meters (115 feet) with alongside depths of 1.5 and 3.0 meters (5 and 10 feet). The second has berthing distance of 22.9 meters (75 feet) with alongside depths of 3.0 and 3.7 meters (10 and 12 feet). The third station at this Greenport Harbor dock has berthing distance of 30.5 meters (100 feet) with alongside depth of 3.0 and 3.7 meters (10 and 12 feet).

Long Island Seafood Export Inc. owns and operates the Greenport Dock to receive seafood and moor fishing vessels. The south part of this Greenport Harbor dock forms the north-side entrance to Rackett's Basin, and there is a fish-processing plant at the rear of the dock. This Greenport Harbor dock has three berthing stations. One has berthing distance of 29.9 meters (98 feet) with alongside depths of 2.4 and 3.7 meters (8 and 12 feet). The second has berthing distance of 24.1 meters (79 feet) with alongside depth of 2.4 meters (8 feet), and the third has berthing distance of 20.1 meters (66 feet) with alongside depth of 2.4 meters (8 feet).

The North Ferry Company owns and operates the Greenport Harbor Ferry Slips as a landing for passengers and vehicles traveling to/from Shelter Island. The ferry boats Shelter Island, Greenport, Islander, and Prospect Dock operate from the Greenport Harbor Ferry Slips. The dock has berthing distance of 27.4 meters (90 feet) with alongside depths of 1.8 and 2.1 meters (6 and 7 feet).

The Greenport Yacht & Shipbuilding Company owns and operates several docks in Greenport Harbor. The Center Dock is used to moor vessels for storage and repair and to moor fishing vessels. A vessel-storage building and shop are located at the rear of the Greenport Harbor Center Dock. With three berthing spaces, the Center Dock has alongside depths of 1.8 meters (6 feet) and 3.7 meters (12 feet). The first berth is 2.4 meters (8 feet) long. The second has berthing distance of 30.5 meters (100 feet). The third berth at the Greenport Harbor Center Dock has berthing distance of 30.5 meters (100 feet).

The Greenport Yacht & Shipbuilding Company also operates the East Dock in Greenport Harbor to moor vessels for storage and repair, to moor fishing vessels, and to occasionally receive fish. Greenport Harbor's East Dock is equipped with two steel rails for the vertical boat lift at the inner end of the bulkhead. A vessel storage building is located at the rear of Greenport Harbor's East Dock. The Dock has three berthing stations. One has berthing distance of 61 meters (200 feet) with alongside depths of 3.7 and 6.1 meters (12 and 20 feet). Another has berthing distance of 45.7 meters (150 feet) with alongside depths of 3.7 and 6.1 meters (12 and 20 feet). The third has berthing distance of 76.2 meters (250 feet) with alongside depths of 1.8 and 3.7 meters (6 and 12 feet).

Greenport Yacht & Shipbuilding owns the Greenport Harbor North Dock, which it operates jointly with the Costello Marine Contracting Company. The North Dock is used to moor vessels for storage and repair, to moor contractors' floating equipment, and to occasionally handle construction equipment and supplies. A shop is located at the rear of the Greenport Harbor North Dock. The berths have alongside depth of 1.8 and 3.7 meters (6 and 12 feet). One berth is 56.4 meters (185 feet) long, and another has berthing distance of 61 meters (200 feet).

The Greenport Harbor West Dock is also owned and operated by Greenport Yacht & Shipbuilding to moor vessels for storage and repair and to moor fishing vessels. Two 500-ton marine railways support the Greenport Harbor West Dock, and there is a shop at the rear. Three berths at the Greenport Harbor West Dock have alongside depth of 6.1 meters (20 feet). The West Dock has berthing distances of 19.8, 92.4, and 96.0 meters (65, 303, and 315 feet). There is also a pump-out station on the inboard side of the Greenport Harbor West Dock with a $5 charge for each tank.

The daytime rate at Greenport Harbor's Mitchell Park Marina, applying from 11am until 10pm, is $1 per foot. Overnight slips at Greenport Harbor's Mitchell Marina Park run from $2.50 to $4.00 per foot from June 15th to Labor Day. Off-season (excluding holidays), overnight rates range from $2 to $2.50 per foot. Additional charges for electricity from $10 to $40 apply to all docks. Boats in need of repair cannot moor at the marina. The marina also has floating docks that can accommodate boats to 21.3 meters (70 feet). Amenities at the Mitchel Park Marina in Greenport Harbor include free television and wireless internet access, bathrooms and showers, potable water at all docks, and a dog walk area.

The Mitchell Park Marina in Greenport Harbor is open from Memorial Day through Labor Day from 8am until 8pm. Other times of year, the marina is open from 9am until 5pm. Greenport Harbor's Mitchell Park Marina is just one minute away from Greenport Harbor's shops, restaurants, and services as well as the trains and buses going to New York and the ferry service going to Shelter Island. The Marina is next door to Greenport Harbor's carousel, camera obscura, and boardwalk.

In the northeast corner of Greenport Harbor, the Brewer Stirling Harbor Marina offers 180 slips and ten acres for boaters seeking sheltered mooring. The marina can accommodate boats to 27.4 meters (90 feet). Located next to the Brewer Yacht Yard, this Greenport Harbor marina offers depths from 2.1 to 3.0 meters (7 to 10 feet). The marina offers water and power, a fuel dock with gas and diesel, and bathrooms and showers. Visitors to the Brewer Stirling Harbor Marina can also get ice and marine supplies, swim in the marina pool, exercise in the gymnasium, or picnic in the area with barbecue grills. This Greenport Harbor offers a complimentary shuttle to the Village of Greenport.

Greenport Harbor's Townsend Manor Inn & Marina offers excellent facilities and service for visitors. With one of Eastern Long Island's best marinas for yachtsmen, the marina has deep-water slips for transient yachts to 16.8 meters (55 feet). Located in Greenport Harbor's Stirling Basin, the Townsend marina is a short walk from the shops and restaurants in the Village of Greenport.

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