How to delete all lists in all webs using PowerShell

You should get rid of foreach loop. Instead directly get the lists from collection and then delete them.

$FruitDocuments = $_.Lists["FruitDocuments"]
 if ($FruitDocuments -ne $null)
 {

        Write-Host($_.Url + "----" +   $FruitDocuments.Title + "------" + $FruitDocuments.BaseTemplate)
        $FruitDocuments.AllowDeletion = $true
        $FruitDocuments.Update()
        $FruitDocuments.Delete()
        Write-Host("Deleted")
 }
 $Fruits = $_.Lists["Fruits"]
 if ($Fruits -ne $null)
 {

        Write-Host($_.Url + "----" +   $Fruits.Title + "------" + $Fruits.BaseTemplate)
        $Fruits.AllowDeletion = $true
        $Fruits.Update()
        $Fruits.Delete()
        Write-Host("Deleted")
 }

UPDATE

Above code may throw error if the list with the given title is not present in a site. The issue can be avoided by using this script:

Add-PSSnapin Microsoft.SharePoint.Powershell

    Get-SPWebApplication https://portal.fruits.com   | Get-SPSite -Limit All  | Get-SPWeb -Limit All | where {$_.Url -Match "crates"}  | ForEach-Object  {

     for ($index = 0; $index -lt $_.Lists.Count; $index++) {
        if ($_.Lists[$index].Title -eq "FruitDocuments") {
            Write-Host($_.Url + "----" +   $_.Lists[$index].Title + "------" + $_.Lists[$index].BaseTemplate)
            $_.Lists[$index].AllowDeletion = $true
            $_.Lists[$index].Update()           
            $_.Lists[$index].Delete()
            Write-Host("Deleted")
        }
        elseif ($_.Lists[$index].Title-eq "Fruits") {
            Write-Host($_.Url + "----" +   $_.Lists[$index].Title + "------" + $_.Lists[$index].BaseTemplate)
            $_.Lists[$index].AllowDeletion = $true
            $_.Lists[$index].Update()           
            $_.Lists[$index].Delete()
            Write-Host("Deleted")
        }
    }
}