I have this colleciton called organization:
[ { \"_id\": \"53a58a02f1001e7fd28f5aec\", \"orgId\": 5,
You can match against fields within an array using dot-notation, so you can simplify your query to:
mongoose.model('organization') .find({'members.user': user}, function(err, usersOrganizations){ callback.send(200, usersOrganization); } );