You can pay it by DD. Just ask your bank (ICICI, HDFC, AXIS or any..) to prepare DD in dollars payable to whatever mentioend in app...
for NY PCC check the below link where all the information for getting PCC state wide there :
http://www.canadainternational.gc.ca/Detroit/offices-bureaux/certificates-certificat.aspx?lang=eng&menu_id=332&menu=L