1.) JFK Airtrain express, Lower Manhattan-Downtown Brooklyn-Kennedy Airport terminals. Operating with the current roomier (for baggage) Airtrain vehicles, perhaps a three Airtrain vehicle train for JFK Airport services.
2.) Commuter service: Lower Manhattan-Downtown Brooklyn-Flatbush avenue-Norstrand ave-East New York-Jamaica.
Transfers to LIRR trains at Jamaica, the Commuter trains would have more commuter style seating (benches), as well as being longer (10 Airtrain Vehicles).
The LIRR-Airtrain Lower Manhattan connection at Jamaica would be a similar set up to the NJ Transit-PATH connection at Newark Penn Station. NJ Transit riders heading to Lower Manhattan or Jersey City transfer at Newark Penn to the PATH.