What is the best way to store a homemade apple pie?

I place a tea towel over the top of the pie. Pies in my house, usually don't last long enough to worry about multi-day storage!

How long are you intending to store it? You can freeze whole pies for quite some time, baked or unbaked. Depending on the size of the pie dish, you might be able to slip the whole thing in a gallon-size zip-top bag. otherwise wrap it nice and tight with foil.

I second Francesca's re-warming via the oven technique. It makes pies taste freshly baked even if it's been stored.

Uncovered? That depends on what comes to your kitchen. Some have cockroaches, some have cats (stories of turkeys eaten by cats on a 'Thanksgiving disaster' question), some have flies, ants, children...
Tupperware?

One of the best apple pie makers, the elegant farmer, suggests leaving their apple pie out on the counter, uncovered.

In the refrigerator until soon before serving and then pop it into the oven for a final warm!