If this 3 hours is the time between flight arrival and flight departure you won't have an enormous amount of time left to visit Amsterdam. I'd be back at Schiphol at least 1 hour before departure time, which leaves 2 hours. The train only takes 15 or 20 minutes, but you will need to build in a bit of a buffer on the way back in case of (not very probably though) delays. So in the end you may have 1 hour 20 minutes left, which is probably still worth it if you've never visited.

I've never really looked at those tours, but you might as well do your own trip with a bit of preparation. And be sure not to get lost in the streets and canals that all look alike (if you're not a regular visitor) and go around in circles