It turns out that a neighbor's hen keeps jumping over the fence into our backyard and this time it laid some eggs. When she left we collected them. Now it's back and laid some more but it won't move out of the way. It's been three days of sitting on them. Is it too late to collect them? If not; how do we collect them without disturbing the hen?

You'll have to wait until she gets up.

It is too late to collect them, you can let her hatch them, little chicks are fun. Should be collected every day.
But you move the hen, reach under her for the eggs,

Too late too collect them? Probably not. My duck's eggs are fine after a fortnight unrefrigerated. But that's assuming that they're unfertilised.
Does your neighbour have a rooster? You don't want to be opeing the eggs if they do.
And collecting eggs from under the hen shouldn't be difficult. Just reach under. It'll either run away or sit idley by while you raid its nest.

As kalfour said, if the eggs are infertile they would be fine,
However if their has been a rooster running free with them well they would not be the best for eating, the egg would have started developing the viens by now and in the middle will be an embryo only very small at an average weight of 0.02gram but their non the less :o yuck lol woldnt fancy a mouthful of that :o
Yo need to find out if there is a rooster that had access to them, as said by others raiding the nest will not be hard...

If you don't want the chickens in your garden yo should speak to the neighbour and ask them to higher the fence so that the bird can not gain access, but in order to stop them the fence would need to be around 8 ft high and an in ward slope so that if they jumped it is harder for them to get over,