Meteor focusses on the developer experience, making it very easy to implement new features in your project. On the other hand, it doesn't provide much flexibility as you cannot choose what technologies you want to use.
The MEAN stack is great, it gives you freedom to do whatever you want, but it requires more configuration and has a higher learning curve. It also doesn't come with realtime updates, optimistic UI, client side database and so much more.
For now I'd go with the MEAN stack, mainly because Meteor doesn't support official server side rendering (SSR) yet which is important for Search Engine Optimization (SEO), it doesn't officially support npm packages (though it will be added in 1.3) and it provides realtime feature you're probably not going to need in your application.