I've got all 100% sync, the only thing missing is the thieves challenges, which I can't finish because I can't find a courier to catch. I know that there's no way to make them "appear", but are there any way to increase the chance for the, appearing, or is there a place or area where they appear more often?
Apparently, couriers don't have any special place where they spawn more, they are simply a rare spawn.
Ubisoft have addressed this in the 1.02 patch that was released for the XBOX and PS3 versions:
Couriers will now appear more often in Boston and New York
I found them to appear more in New York, but I've only seen 3 so far in all my game time.
Unsurprisingly they always appear when I'm busy with other things, so I have to break off and chase them down. They are a 'rare' spawn though, with some people saying they show up after you pay off a printer.
There is a spot listed here, with a confirmation post.
However I've not tried this spot myself.
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The place I remember them spawning more than once is in the market that is in the middle of broadway.