I managed to get somewhat what I needed from the native api.
I wrote this script which displays the sum of each image layers, grouped by package

$key = "<key with native api access>"
$uribase="http://<proget server>/api/json/"
$feedid = <feed id>
$packages = Invoke-webrequest "$($uribase)DockerImages_GetRepositories?key=$($key)&Feed_ID=$feedid" | select -expandproperty Content | convertfrom-json

$size_lookup = @{}


$data = @()
$total = $packages.length
$count = 0;
$packages | %{
	$n = [uri]::EscapeDataString($_.Repository_Name)
	$progressPreference = 'silentlyContinue'
	$images = Invoke-webrequest "$($uribase)DockerImages_GetImages?key=$($key)&Feed_ID=$($feedid)&Repository_name=$n" | select -expandproperty Content | convertfrom-json
	$progressPreference = 'Continue'
	$images | %{

		$manifest = [System.Text.Encoding]::UTF8.GetString( [Convert]::FromBase64String($_.ManifestJson_Bytes) ) | convertfrom-json
		$layers = $manifest.layers
		$sizesum = $layers | ?{$_.size -ne $null } | measure -sum size | select -ExpandProperty sum
		$obj = @{}

		$obj.Add("Feed",$_.feed_id)
		$obj.Add("Repository",$_.Repository_name)
		$obj.Add("Manifest",$manifest )
		$obj.Add("Layersum", $sizesum )
		$obj.Add("DownloadCount",$_.Download_Count)
		$obj.Add("Published",$_.Published_Date)
		$data += $obj

	}

	$count++
	write-progress -PercentComplete ($count*100/$total) -Activity "Working..."
}

$data | convertto-json -depth 99 | set-content -encoding utf8 out.json

$data | group-object Repository | %{
	$s=$_.group | measure -sum layersum | select -ExpandProperty sum;
	$n = $_.name;
	new-object psobject -Property @{"name"=$n;"size"=$s}
} | sort-object size

Dealing with a low disk space situation, I'm having trouble locating which docker packages are taking up space. I know from the "manage registry" page that the whole feed is taking up some 99% of the disk, which isn't really helping me.

I need to know how much disk space is claimed by each package - each of which can have hundreds of tagged versions. Is this information available anywhere?