I've been doing research on the New Netherlands, and among other things happened upon mention of the flag that flew over the colony: that of the Chartered West India Company, the Geoctroyerde Westindische Compagnie in Dutch. So, first off, here's a Google Docs link to my take on a Northern Crown version of it. In case you prefer a version using the "Nederlander Northern Crown Company" name given in the Gazetteer to my retention of the "Chartered" part, try this link. Contrary to how it's often presented online, my research suggests that the flag flown at the time bore an orange stripe, not the later red stripe.
The seal of the colony as a whole requires no modification:
But the seal of Nieu Amsterdam requires a bit more work to modify the GWC at the top, beyond my digital editing abilities. Check here for a photo of a page with the image and some description.