$siteCollectionUrl="http://sp2013/sites/team"
$templateNamesToRemove = "COMMUNITY#0","COMMUNITYPORTAL#0"

Start-SPAssignment -Global
$web = Get-SPWeb $siteCollectionUrl

# get the existing web templates from the site that will be filtered down
# 1033 is the locale id for English US (en-us), be sure to change to your locale
$existingWebTemplates = $web.GetAvailableWebTemplates(1033)
$newWebTemplates = New-Object "System.Collections.ObjectModel.Collection[Microsoft.SharePoint.SPWebTemplate]"

# filter existing web templates and only keep if in the list of template names to keep
$newWebTemplates = $existingWebTemplates | Where-Object {$_.name -notin $templateNamesToRemove}
$web.SetAvailableWebTemplates($newWebTemplates, 1033)
$web.Update()

Stop-SPAssignment -Global