The money that trade missions give, IIRC, is based on the value of a theoretical trade route from the city you conduct the trade mission in to your capitol. Anything that increases the value of a city's trade routes (high pop, Temple of Artemis, Harbor, being on another continent, etc.) will boost the money you get from a Great Merchant trade mission. In my (admittedly limited) experience, however, it's not a very large difference either way. Sending your GM to the nearest, biggest capitol/coastal city with a Harbor will generally yield enough money to make sending him to the other side of the world for the Temple of Artemis not worth it.
There's a way to check how much money you can get from a trade mission without committing the GM's turn, though. If I remember right hold Shift, click on the "Go To" command and left-click on the city you want to inspect. The game will cue the move order and wait for you to cue another command, which includes the option to conduct a trade mission in that city. Keep holding shift the entire time, and simply hover the mouse over the trade mission button to see how much it's worth. If you don't want to commit the cued move order hit the cancel button to cancel it, then let go of shift. Otherwise, let go of shift before hitting cancel, and the GM will proceed with the move order.