DB - I can't speak to closing costs or taxes in NY, but can about settling and "other". All houses settle to some extent. Building codes are designed to minimize problems by specifying footing sizes, etc. for various types of soil.. New home warrantees are designed to deal with the the issues that arise when settling occurs, as well as other problems. Different states have different laws about the timeframes and extent of warrantees. Make sure you have one, and you understand what it covers!
Other things to beware: exactly what is and is not included in the cost? What will your allowances cover? What kind of landscaping? Sod in front, or all around? ? Driveway/walkway paving? Fencing? A deck, or just a header for one? Patio(s)? You can easily run up costs by upgrading and thus exceeding allowances for light fixtures, flooring, number of paint colors, door hardware - the list is as long as the number of parts in a house. The more detailed your specifications (right down to part numbers), the more accurate your builder's estimate can be.
Enjoy the process - and best of luck with your brand new home!