It depends on a few things: what kind of Pokemon you need on your team(bulky, really fast sweeper,...) and if you need a physical of special attacker more.
It's not that one is just really better than the other, which is the case with most Pokemon you can compare like that, comes down to personal preference and what you need.
The being said, Mewtwo Y is a fast special sweeper while Mewtwo X is a bulkier(still fast) physical attacker and not much is really stopping it from being a sweeper as well.