One problem atm is, that all "trading" is done by Boston. So there is no need for cities to trade with eachother and therefore no need to transport goods. So there is no need for infrastracture, and no raiding of transports. So here is the suggestion:
The boston trading company auctioneers trading rights for cities. For every 300 players active on the server one trading right is sold to the highest bidder. This right makes it possible to build a marketplace which establishes a safe-zone (the marketplace only) where player can build market stalls. The city itself can not use the marketplace to store things, think of it as a embassy of the boston trading company, but does get a percentage of sales generated. It also works as a teleport point. Players no longer have free travel to Boston but to the nearest town with a marketplace. The contract period is four weeks - after that the marketplace gets closed if trading-rights are bought again.