So we’ve studied the timetables offered by the LIRR and discovered, thankfully, the Amtrak emergency repairs at Penn Station will not effect the connections to the ferry. The LIRR arrivals and departures at Sayville Station very slightly due to the engineering work from July 10 to September 1. This will make connecting from/to Sayville Ferry a bit tighter. The Fairy Schedule has been updated to reflect these minor adjustments.
Here are all the LIRR details if you’re interested.

Discounted fares are available from Atlantic Terminal, Hunterspoint and Jamaica Stations.

If you want to avoid Penn station all together here are a few suggestions.

  • Head over to Atlantic Terminal in Brooklyn via subway lines 2,3,4,5,B,D,N,Q,R. Departures and arrivals at Atlantic Terminal are detailed in The Fairy Schedule. Additional info from LIRR hereLIRR ticket holders can transfer for free at certain key locations during the morning rush.
  • Direct trains to Babylon are available at Woodside LIRR station via the 7 train. Use this Trip Planner (Woodside Station to Sayville Station, or back) here.
  • Rush hour ferry service from/to East 34th St to Hunterspoint and  Long Island City Stations will connect to Jamaica and Babylon bound LIRR trains. Additional info from LIRR here.

To get up-to-the-minute updates on schedule and service changes, sign up for MTA Alerts and text messages at www.mymtaalerts.com, follow @LIRR on Twitter and/or download the LIRR’s Train Time® app.

For Friday evening arrival at Fire Island, the best and likely simplest way to avoid Penn Station is to depart from the E 34th Street Ferry Terminal.  It’s direct service from Long Island City Station to Sayville on Fridays only.

 
NYC to Cherry Grove and The Pines on Fridays
To Meet this FerryDPT 34th St LIRR FerryConnects toNotesARR SayvilleTime to FerryTravel Time
Friday 6:30 PMDPT 4:11 PM, ARR 4:16 PMDPT 4:28 PM
Short walk to LIC LIRR Station*
Direct to Sayville, Peak Fare6:07 PM00:2302:39

*Here’s a map for the 4-minute walk from the ferry landing to the LIRR station.

When the NYC Ferry Astoria service starts in August, it will provide an easy way to connect with Wall Street.