Brand New 2 Stories House vibrates when it's windy
Complain to your builder (try to have them visit on a windy day) and ask what they can or will do about it. 

The next step is probably:

Plant trees to provide a windbreak. Without knowing where you are, a general suggestion would be something fast-growing but not, perhaps, the tree you'd love to have mixed with trees that grow slower and have more desirable properties - hybrid poplars being a prime example of the first type - they grow fast, and you probably won't mind cutting them down when the other trees grow more and fill in - but they do grow fast.



If you have a high budget I suppose you could try building a fence high enough to impact the wind on the second story, but that's an expensive proposition. Fencing for windbreak should be about 25-50% open, not solid; a solid fence diverts it up, and the air currents downwind can be worse than without a fence - a partially-open fence (or tree branches) slows it down more effectively.

Farm-oriented but fairly understandable wind mitigation info from Purdue.

An example of a large commercial wind fence.