Not trying to be a dick, andI know the phrase, if you have to ask you can't afford it, but when a provider says, my outcall rate to you is X plus transportation costs, how do you handle it?

a $1000/hr hooker is going to gouge you on transportation?  I would recommend asking her if she plans to come by car, train, or helicopter, and then google prices so you have an idea of what to expect, at least within plus or minus $50.

but if you are asking her to travel, it's only right to compensate her for it. At least she isn't charging travel time.

You have to estimate where she is coming from, or use the location stated in an Incall ad.  Offer a reasonable amount and in a polite way say take it or leave it.  If this figure does not cover what she needs, she will have to give you more detail on where she is coming from.

just go to New York..problem solved..

rates posted on their websites. Even if your particular gal doesn't, you can still use knowledge of what others charge to get a sense of what you're in for (assuming she isn't intent upon gouging you).

"drill a well" a euphemism for sex, and if so, since when do the girls pay YOU?

but I only charge when the depth I drill is measured in the hundreds or thousands of feet, and not by the inch. lol

Depending where you are in NYC and where she is coming from, she might have to pass a few tolls on the way.  I've read NYC collects a million dollars in tolls every day.   That's a billion dollars every three years.  

MTA toll revenue in 2015 alone was around $1.8 billion! MTA expenses in 2015 were around $452 million.

Tell the provider that she will need to submit an itemized expense report for her travel costs, and once you have reviewed the receipts and checked her math, you will issue a check for that amount. Otherwise, this ridiculous business practice gets into some silly details, like you guessing low on the cost or her not being able to make change.