I want to get list of all libraries along with sizes ( including permissions if possible) in top level site collection and also there is subsite under this , I need same information for the subsite.

Is there any way we can get it through or some third party tools. Please he

if you need third party means Check Sharegate http://en.share-gate.com/sharepoint-management

Also I hope it can be done by PowerShell with little effort

http://www.sharepoint-journey.com/get-all-document-libraries-in-a-site-collection.html

Thanks Pravin, I am talking about free third party tools.

Also can you please provide powershell script.

I have no idea about Free tools.

http://tomvangaever.be/blogv2/2013/03/powershell-script-to-list-all-lists-and-libraries-with-unique-permissions/

above site give script for  get all the list with unique permission. I have do small change for get all the list. I am not yet test the changes so please check if any error please let me know.

01.cls  
02.Write-Host "********************************************************************"  
03.Write-Host "| This script will check all list  |"  
04.Write-Host "********************************************************************"  
05.Write-Host  
06.Write-Host "Loading Microsoft.SharePoint.PowerShell..." -ForegroundColor Yellow  
07.Write-Host  
08.  
09.Add-PSSnapin Microsoft.SharePoint.PowerShell -erroraction SilentlyContinue  
10.  
11.$siteURL = Read-Host "Please provide url of the SiteCollection"  
12.$loglocation = Read-Host "Please provide path for the log file (hit ENTER to not store output)"  
13.$site = Get-SPSite($siteURL)  
14.  
15.Write-Host  
16.if($loglocation -ne ""){  
17.    start-transcript -path $loglocation  
18.    Write-Host  
19.}  
20.  
21.Write-Host "--------------------------------------------------------------"  
22.  
23.$counter = 0  
24.Write-Host "The following lists and libraries  `r`n (results marked in Red might have an 64K ACL impact):" -ForegroundColor Yellow  
25.Write-Host  
26.  
27.foreach($web in $site.AllWebs) {  
28.    foreach($list in $web.Lists) {  
29.          
31.            $counter = $counter + 1  
32.            if($list.ItemCount > 1500){  
33.                Write-Host $list.DefaultViewUrl "- ItemsCount:" $list.ItemCount -ForegroundColor Red "`r`n"  
34.            }else{  
35.                Write-Host $list.DefaultViewUrl "- ItemsCount:" $list.ItemCount "`r`n"  
36.            }  
37.         
40.    }  
41.}  
42.Write-Host "--------------------------------------------------------------"  
43.  
44.if($counter -lt 0){  
45.    Write-Host $siteURL "has no lists or libraries !" -ForegroundColor Green  
46.}else{  
47.    Write-Host $siteURL "has $counter lists or libraries !"  
48.}  
49.Write-Host "--------------------------------------------------------------"  
50.  
51.if($loglocation -ne ""){  
52.    Stop-Transcript  
53.}  
54.Write-Host