App store is the only source to updating (through Commandline or directly) Xcode or others apps.If store itself no updation of app.Then probably have to wait for it instead of installing another version from Apple download section.
Yes.Sometimes it happens to me.App store not showing new version of Xcode in Updates Tab.So i m going directly to search Xcode.
My current Xcode version is Xcode 8.3.3 But App store shows only stable version as latest version (currently Xcode 8.3.3) If you wanna more latest beta version product You can get from below From Apple Downloads section

i checked via command line also using below command But the result is same. softwareupdate --list to see what's available.
Result :
Apples-Mac-mini:~ apple$ softwareupdate --list Software Update Tool Finding available software Software Update found the following new or updated software: * macOS Sierra Update-10.12.5 macOS Sierra Update (10.12.5), 873261K [recommended] [restart] * RemoteDesktopClient-3.9.3 Remote Desktop Client Update (3.9.3), 8587K [recommended] * iTunesXPatch-12.6.1 iTunes (12.6.1), 179760K [recommended] Apples-Mac-mini:~ apple$
You can updated Xcode or other software if it's available using below command
softwareupdate --install <product name>
You can get more comments from here Software update tool