which one is prefered to use in 1.3.1?
Use the npm one. From (the upcoming) Meteor 1.3.2 onwards, meteor’s jquery package will prefer it too if it’s installed.
(Be aware, however, that if you don’t already have the npm one installed (for your app or another npm package that needs it), adding it in 1.3.1 means jQuery will get loaded twice, and potentially, extensions will get added to either (but not both) of these separate jQueries. If that bothers or affects you, you could use just the Meteor one if that’s possible, until 1.3.2 is out. And even after upgrading, you could even continue to depend on the meteor one and simply install the npm one, which will have the same affect - since as said above, meteor 1.3.2+'s jquery will prefer npm’s jquery if it’s already installed).
use meteor’s package system until it dies.