I would prune... now is the time to set the future growth pattern/shape of the trees and get things going in a direction you really want. I've learned the hard way for being overly cautious. You can be aggressive with pruning early on and it will only benefit the tree in the long run. Now I walk up to young beautiful & tall apple trees in my nursery and often top them back down a couple feet.
I lieu of a larger cage which bigger is always better in my opinion ... simply because a larger cage will let some of those lower branches grow out with better crotch angles and you could try and pull down the lower ones (maybe they are big enough that you may damage the tree sometimes they do often bend down enough to improve the branch (weighted or tied down) without breaking).
I like lower branches (people have different ideas on this - there is no real right answer) on my deer apple trees for one reason - bucks cant get into rub the trunks once I pull the enclosures. So a large cage to me is more ideal but...... Im tightening up my fence diameter just due to costs and with that comes those higher up "lower" branches - great for mowing around but bad due to bucks potentially rubbing the trunks AND....... they will. I have pics! I know lower branches are a hassle to deal with but they are protection for the tree... and plan on keeping the window screen on for as long as you can - years longer than you think you should.
So the apple tree ... I would likely do this - with a bigger cage I would pull the left limb down; with your cage I would cut the left limb at what looks like a branch coming off that limb, I would cut the lower right mess you got going on totally off. I would pick one of the three leaders at the crown to keep and cut the others back for scaffold branches and let the best one run as the central leader. In this case I think if you keep what you have you'll be fighting an open center type approach and the tree will suffer in the long run. Get cut happy and do your tree a favor.
Its always a gamble but I think its a start. The above is just an opinion -- the fun is picking a path and wondering if it was the right way. Read up on nicking the trunk to promote lateral branching if none of those side branches take off growing. I wont say more on that because I have not mastered that at all yet.
The pear like others mention they like to grow straight up - I struggle with the few trees I do have on what to do.