Of course, there are timestable for Metropolitan Transportation Authority which handles Subway, Bus, Staten Island Railway, Metro-North and Long Island Railroads. It also handles Long Island Bus.
However subways and buses never on time.
Subway, buses, Staten Island Railway, Long Island Bus, Roosevelt Island Tramway, and WCDOT Bee-Line Buses are $2.25, premier express buses $5.50 and Bee-Line BxM4C are $7.50 one way.
JFK Airport to Times Square.
Quickest way to slow way.
Option 1: Airtrain JFK/Long Island Railroad.
Step 1: Take Airtrain Jamaica to Jamaica Station.
Step 2: Look for green LIRR Ticket Vending Machine and purchase $5 MetroCard with Jamaica to Penn Station for $8.75 peak, 6.25 off-peak, $3.75 Weekend CityTicket. $5 to exit system.
Step 3: Take westbound LIRR to Penn Station.
Step 4: Once at Penn Station, go to MetroCard Vending Machine at 7th Av Subway Station in refill a MetroCard to $2.25. Or depends how long you spend, you have buy seperate Unlimited MetroCard because you cannot refill Unlimited MetroCard on regular MetroCard.
Option 2: Airtrain JFK/Subway:
Step 1: Take Airtrain Jamaica to Jamaica Station. Get $5 MetroCard to exit system.
Step 2: Go downstairs to Sutphin Blvd-Archer Av subway station. If you're staying longer, purchase Unlimited MetroCard.
Step 3: Take Manhattan-bound (E) express to 42nd St-Port Authority Bus Terminal, which is connected to Times Square Station.
Please note during late night, when (R) only operates as Brooklyn Shuttle, (E) runs local for entire length after 11:30pm.
Newark Airport to Times Square.
Faster way to slow way:
Please note $5 surcharge occurs on onboard New Jersey Transit commuter trains when ticket machine is working or ticket windows are opened.
Option 1: Via Airtrain Newark/NJ Transit Train
Step 1: At you terminals, look for orange New Jersey Transit Ticket Vending Machine and purchase $15 one way ticket to New York Penn Station. You need to hold onto it because $5.50 AirTrain fee is enconded in this ticket.
Step 2: Take Airtrain Newark to Newark Liberty International Airport Station.
Step 3: Take New Jersey Transit's inbound Northeast Corridor or North Jersey Coast Line to Penn Station.
Step 4: Then transfer to NYC Subway uptown (1)(2)(3) to Times Sq-42nd St. It's best if you buy Unlimited MetroCard at subway station if you're staying longer.
Option 2: Via Bus/PATH:
Step 1: Look for New Jersey Transit #62 bus stop outside your terminal. Make sure destination goes to Newark Penn Station. Why? Perth Amboy-bound bus also shares stop. New Jersey Transit Buses are based on fare zone.
Step 2: Paid $1.50 one-zone fare to ride to Newark Penn Station.
Step 3: Purchase $1.75 Single Ride PATH MetroCard to enter PATH train.
Step 4: Take World Trade Center train to World Trade Center.
Step 5: Once at World Trade Center, follow sign to (A)(C)(E)(1)(2)(3) Complex at Chambers St-World Trade Center-Park Place.
Step 6: Buy Unlimited MetroCard if you're staying longer.
Step 7: Take uptown (A) express, (C)(E) local to 42nd St-Port Authority Bus Terminal.
Option 3: GoBus28/Newark City Subway Lightrail/New Jersey Transit
Please note GoBus#28 is express version of #28 Local bus and this special bus you MUST EXIT AT REAR DOOR. For your convience, there is luggage rack by front door.
Step 1: Outside ground level, look for GoBus#28 Bus Shelter and wait for GoBus#28 heading to Bloomfield Station via Broad Street Station, not via University Heights.
Step 2: Paid $2.20 ($1.50 one-zone plus 70 cent fee transfer) to purchase transfer.
Step 3: Take GoBus#28 via Broad St to Broad St Station.
Step 4: Cross street to Broad St Station and Newark City Lightrail to Newark Penn Station. Transfer slip are consider proof-of-payment and New Jersey Transit law enforcement officer will check your ticket or transfer to see you have valid ticket.
Step 5: Then look for NJ Transit Ticket Vending Machine and purchase one way ticket to New York Penn Station $5 and take inbound Northeast Corridor or North Jersey Coast Line to New York Penn Station.
Step 6: Once at Penn Station, purchase Unlimited MetroCard at subway station and take uptown (1)(2)(3) to Times Sq-42nd St.
Official Port Authority of NY & NJ http://www.panynj.gov
PATH train Port Authority TransHudson http://www.panynj.gov/path/
AirTrain JFK http://www.airtrainjfk.com
Long Island Railroad
Subway Map and Service Guideline