Hey, its quite simple.
Label in leaflet displays a message when hovered over markers in the map whereas popup displays message when clicked on the marker. Both are used within Marker functions.
Ex: In the belw example, The below message is showed by label and the upper message is popup message when clicked on the marker.
long = c(77.6944,77.7141,77.679907)
lat = c(12.9811,12.9675,13.0118285)
label = c("My Office","My College","My House")
add = data.frame(label,long,lat)
m <- leaflet(add) %>% addTiles()
m %>% addMarkers(label = ~label,popup = ~label)