I think you maybe asking two separate sets of questions: 1) What are recommended settings and conditions for the best photo and 2) What is the best format to ensure longevity of the digital file?

For 1) it depends on your subject, but otherwise I suggest reading on product shot information or better yet, hire a professional photographer that shoots similar shots for a living. They could recommend the best conditions, lighting, camera settings and other items, which will vary by location, subject, lens, etc. Having an experienced professional, on site, and available to analyze the final images would be a good spend of money and time, and will ensure that you have the best conditions for your subject and location.

As for 2), this represents a significant issue. Not only must you concern yourself with the file and file reading capability, but also the media. 500 years is a significant timeline. Given your timeline, I do not think any file format will be preferred over others. IMHO, likely any of them will be lost to time, forgotten and be unreadable in that timeline.

The Library of Congress (LoC) might be a valuable resource, and perhaps you should consider their approach: They preserve the original as current knowledge advises, and constantly improve their methods over time. They never store and forget. In addition they are constantly updating to the latest storage methods, for example digitally scanning, and also converting those scans to newer formats as time goes on. Most importantly, the LoC also preserves the devices needed to read those artifacts.

Edison invented the phonograph, and recordings sold by his company and others were wildly popular. Many of these earliest recordings are preserved in the LoC. Yet there are likely very few readers of this answer that can listen to the Edison Phonograph recordings, because those were recorded on wax cylinders, not records as we know them. Records did not become popular until they were standardized in the 1940s. So, in less than 100 years, the ability to play the original format had all but disappeared and is rarer still today.

So, picking the most popular format is no guarantee of success. I would recommend picking a non-proprietary format, save and maintain the equipment needed to read and access those files and then put in place processes to maintain other more current formats of the original over time. NEF obviously is proprietary to Nikon, and the specifications of the format are not published. While the TIFF specification is technically owned by Adobe, they allow its use broadly, publish the format openly and it is well supported by software and hardware today. TIFF is included in the LoC recommended format standards. But, your plans should include maintaining a computer or other device capable of reading, displaying and digitally transferring those images for future generations to convert into modern future formats.