I don't have access to your data, so I am shooting blind.
However, when I consider your leaflet call like this (see below) I don't see any basemap being added. So a display with no basemap is actually the expected behaviour 
lf_clergy <- leaflet() %>%
addMarkers(spdf,
lng = spdf$lon,
lat = spdf$lat,
markerClusterOptions())
lf_clergy
Would something like this (see below) work any better?
lf_clergy <- leaflet() %>%
addProviderTiles("Stamen.Toner") %>%
addMarkers(spdf,
lng = spdf$lon,
lat = spdf$lat,
clusterOptions = markerClusterOptions())
lf_clergy
To elaborate a bit further consider this reproducible example using three NC cities:
library(sf)
library(leaflet)
points <- data.frame(name = c("Raleigh", "Greensboro", "Wilmington"),
x = c(-78.633333, -79.819444, -77.912222),
y = c(35.766667, 36.08, 34.223333)) %>%
st_as_sf(coords = c("x","y"), crs=4326)
# no basemap was specified, and none is shown
leaflet(data = points) %>%
addMarkers()
# a basemap was specified, and so is shown
leaflet(data = points) %>%
addProviderTiles("Stamen.Toner") %>%
addMarkers(clusterOptions = markerClusterOptions())
A shameless plug in: a while back I wrote a long form blog post about using {leaflet} in R, including cluster options. In case you find the topic interesting you can have a look here: https://www.jla-data.net/eng/leaflet-in-r-tips-and-tricks/