The cherry tree needs very little pruning, just pinch out the tips of the main leading branches and cut out any branches that cross over the centre of the bush. You would normally do this in the spring before the buds burst, but you can do it now (if you seal the cut branches with pruning sealant) if the tree looks very overcrowded with misplaced stems. Cherry trees do tend to be rather leggy by nature, so I don't think there is anything wrong there.
Is the pear tree being grown as a bush or as a pyramid shape? The pruning is slightly different to maintain the different shapes, but it consists of a little summer pruning and a little in winter for both types.
Providing the pots are strong enough, there is no reason why they should not stay outside over winter unless, of course, the temperature falls to ridiculously low levels. The trees are perfectly happy to be outside and will need pollinating insects to visit them in the spring.