First the likely causes of your apples problems.
Holes in apples where you then find a maggot inside them is caused by the Codling Moth.
She lays here eggs on the surface of the fruit in the summer months and the resulting critter burrows into the fruit and munches away until you take a bite.
To stop mum laying is the best way organicaly to deal with her.
If you hang a Codling Moth Pheromone trap in the tree you have a fair chance of catching the males of the moth before they have a chance to mate with the females.
( The trap gives off the scent of the female Codling and fools the male into thinking he has found a mate....he then gets stuck on the traps sticky surface.)
It will not get all of them , but it could at least bring the numbers down to avoid spraying.
There are organic controls but as you can see from this article...it ain't easy.
As regards the misshaping.
Several main reasons available.
Poor pollination will cause distortion of the fruit as the side that is carrying the fertile pips will grow much larger than the other side.
Frost damage will cause severe distortion.
Aphid damage when the fruit is very small....especially Woolly Aphid and Rosy Apple Aphid.
Finally if there are brown lesions on the fruiit as well this is Scab and that too can distort the apple.
Organic aphid control is with Surfactants.( Soaps ). but both Woolly and Rosy Apple types may need a little hand painting with some form of spirit...Meths. for e.g.
Scab, other than suggestions below, Organicaly...Sulphur dust or spray or Neem oil.
Good hygine around the tree will help to keep a lot of problems under some control.
Sorry this is so long winded...but tried to covor all the likely causes.
Remove dead and dying wood. Rake up leaves and burn.
Prune the tree so it has good light and air movement through it.
An apple a day.....keeps me in work.