Philly to JFK?
 

I know a lot of people had asked about this in the past, but I just want to ask for more clarification and suggestions.
Which is the best route to reach JFK, I was think about taking a bus to NY then use the subway, but which bus is the best to use? (Stop near subway station with direct train nearby)
Also, just curious if the China Airline shuttle is just for those who fly with China Airlines? My flight time is similar, so I was wondering if I can use it.

PHL is close to the 30th St Amtrak station. From there take the train to Penn Station NY, then LIRR to Jamica and Airtrain to JFK.

But Amtrak will typically cost more than the bus.

OP: look for a bus that goes into Manhattan's Port Authority Bus Terminal, from which there is easy access to the Queens-bound "E" subway, which will take you to the JFK AirTrain station in Jamaica (subway stop "Sutphin/Archer/JFK").

Define best.

You can arrange for car service from Philadelphia to JFK, door to door with no hassles of handling luggage on multiple trains/buses/subways.

$39 or less on Amtrak saver fares. The train route is middle of the road, in terms of comfort, reliability, ease, etc. I can't comment on the bus from Philadelphia, but I would not recommend the NYC subway, especially if the OP has a lot of luggage and/or traveling on weekends.

Many variables.

What time is your flight?
When are you planning to arrive in NYC? Day of the week and time of day will change my answer.
Luggage?
Able bodied?
Departing from PHL airport or Philly the city?