I am not a descendant of the Berry line. Rather, one Berry married into my family. I usually do a bit of research on in-laws and traced the Berry family into Wisconsin.
Regarding Daniel's place of birth... If you examine the census records for Daniel's 3 sons you will see that they consistently list their birthplace and the birthplaces of both parents as New York.
Regarding Nicholas's death certificate, keep in mind that information on a Death Certificate is only as good as the knowledge and memory of the informant... in this case, Nicholas's wife. (I have seen incorrect information on Death Certificates before.) One example, this cert lists his mother's name as "Anna" which does not match the name "Mary" which appears on census records with the 3 sons. (But perhaps Mary was a stepmother - certainly possible.) So, the question is...how likely is it that Nicholas's widow remembered (or knew) the correct information.
But these census records for Dan's sons all list NY as the birthplace:
Thomas - 1880,
Nicholas 1880, 1900 and 1910,
and Charles 1880 and 1900.
In this case, it seems much more likely that the 3 men themselves would know and correctly remember their parents' birthplaces.
My money is on NY as Daniel's birthplace.