Variation of https://gist.github.com/oscarperpinan/5451682 using SpatialPolygons

stamenPoly.R

library(sp)
library(ggmap)
## latticeExtra must be loaded after ggmap because both ggplot2 and
## latticeExtra define a 'layer' function. We need the definition from
## latticeExtra.
library(latticeExtra)
## We only need maptools to get an example
library(maptools)
SIDS <- readShapePoly(system.file("shapes/sids.shp", package="maptools")[1],
                      IDvar="FIPSNO",
                      proj4string=CRS("+proj=longlat +ellps=clrk66"))

## Get the stamen map. Same as with SpatialPoints
bbPoly <- bbox(SIDS)
gmap <- get_map(c(bbPoly), maptype='watercolor', source='stamen', crop=FALSE)
bbMap <- attr(gmap, 'bb')
latCenter <- with(bbMap, ll.lat + ur.lat)/2
lonCenter <- with(bbMap, ll.lon + ur.lon)/2
height <- with(bbMap, ur.lat - ll.lat)
width <- with(bbMap, ur.lon - ll.lon)

## Use latticeExtra::+.trellis and latticeExtra::layer instead of sp.layout
spplot(SIDS['BIR79']) +
                  layer(grid.raster(gmap,
                                    x=lonCenter, y=latCenter,
                                    width=width, height=height,
                                    default.units='native'),
                        under=TRUE)

stamenPolyWithLayerInFunction.R

## If you need to use layer inside a function, you have to evaluate the code inside "layer({})" 
## or pass the arguments as a list in 'data'.
myFoo <- function(){
    spplot(SIDS['BIR79']) + 
        layer({
            bbPoly <- bbox(SIDS)
            gmap <- get_map(c(bbPoly), maptype='watercolor', source='stamen', crop=FALSE)
            bbMap <- attr(gmap, 'bb')
            latCenter <- with(bbMap, ll.lat + ur.lat)/2
            lonCenter <- with(bbMap, ll.lon + ur.lon)/2
            height <- with(bbMap, ur.lat - ll.lat)
            width <- with(bbMap, ur.lon - ll.lon)
            grid.raster(gmap,
                        x=lonCenter, y=latCenter,
                        width=width, height=height,
                        default.units='native')
        }, under=TRUE)
}

stamenPolyWithLayerInFunction2.R

myFoo2 <- function(){
    bbPoly <- bbox(SIDS)
    gmap <- get_map(c(bbPoly), maptype='watercolor', source='stamen', crop=FALSE)
    bbMap <- attr(gmap, 'bb')
    latCenter <- with(bbMap, ll.lat + ur.lat)/2
    lonCenter <- with(bbMap, ll.lon + ur.lon)/2
    height <- with(bbMap, ur.lat - ll.lat)
    width <- with(bbMap, ur.lon - ll.lon)
    
    spplot(SIDS['BIR79']) + 
        layer({
            grid.raster(gmap,
                        x=lonCenter, y=latCenter,
                        width=width, height=height,
                        default.units='native')
        }, under=TRUE,
              data=list(gmap=gmap,
                  lonCenter=lonCenter, latCenter=latCenter,
                  width=width, height=height))
}

stamenPolyWithLayerInFunction3.R

myFoo3 <- function(poly){
    bbPoly <- bbox(poly)
    gmap <- get_map(c(bbPoly), maptype='watercolor',
                    source='stamen', crop=FALSE)
    bbMap <- attr(gmap, 'bb')
    latCenter <- with(bbMap, ll.lat + ur.lat)/2
    lonCenter <- with(bbMap, ll.lon + ur.lon)/2
    height <- with(bbMap, ur.lat - ll.lat)
    width <- with(bbMap, ur.lon - ll.lon)
    
    spplot(poly) + 
        layer({
            grid.raster(gmap,
                        x=lonCenter, y=latCenter,
                        width=width, height=height,
                        default.units='native')
        }, under=TRUE,
              data=list(gmap=gmap,
                  lonCenter=lonCenter, latCenter=latCenter,
                  width=width, height=height))
}

myFoo3(SIDS["BIR79"])

stamenPolyWithLayerInFunction4.R

myFoo4 <- function(poly, map, ...){
    bbMap <- attr(map, 'bb')
    latCenter <- with(bbMap, ll.lat + ur.lat)/2
    lonCenter <- with(bbMap, ll.lon + ur.lon)/2
    height <- with(bbMap, ur.lat - ll.lat)
    width <- with(bbMap, ur.lon - ll.lon)
    
    spplot(poly, ...) + 
        layer({
            grid.raster(map,
                        x=lonCenter, y=latCenter,
                        width=width, height=height,
                        default.units='native')
        }, under=TRUE,
              data=list(map=map,
                  lonCenter=lonCenter, latCenter=latCenter,
                  width=width, height=height))
}

mapWater <- get_map(c(bbox(SIDS)), maptype='watercolor',
               source='stamen', crop=FALSE)

myFoo4(SIDS["BIR79"], mapWater,
       col.regions=terrain.colors(30))

mapTerrain <- get_map(c(bbox(SIDS)), maptype='terrain',
                      source='stamen', crop=FALSE)

myFoo4(SIDS["BIR79"], mapTerrain,
       col.regions=terrain.colors(30))

Watercolor stamen maps are now in jpeg format. Version 2.4 of ggmap fixes this: dkahle/ggmap@d657e1c.