please specify a geographical region thx!

Without ever having looked into it with a degree of depth, they weren't clean. Overcrowding and unsanitary conditions in rapidly growing cities notoriously contributed to the spread of the plague. Off the top of my head, I recall some rather indecorous descriptions of the 1348 plague in Florence and Paris: Boccaccio writes about the strong stench of rotting bodies prevalent throughout the town, the bodies to be found in the street as well as in their homes. Consider also that there would be animals in the street, so a scene where pigs, or stray dogs, would be investigating a body deposited in the street is entirely plausible. At the same time, there was a gravedigger's 'guild' of sorts that supposedly took care of the dead and decomposing bodies. Alistair Horne writes similar things of Paris in 1348, where bodies were also to be found in the street, stench, etc. The Parisians also apparently took on the idea of killing cats as they believed them to be carriers of the plague (rather than the rats which the cats killed).

Later in the 14th century Paris was expanded significantly by Charles V. London also grew over to the south bank of the Thames during the 14th century. The bigger cities and smaller post-plague populations would would have certainly helped the cause of (relative) cleanliness. Even so, Paris would be largely be a wood-and-mud type city until the end of the 16th century when Henri IV began transforming the city into one of stone.