I usually end up fiddling around in Excel, planning out time and costs for many different ways to get from A to B..
    EWR -> MIA
    EWR -> FLL
    JFK -> MIA
    FJK -> FLL
   ... etc ..

What are you talking about? Every major travel website has an option along the lines of 'New York City - All airports', which includes JFK, LGA, EWR