Congratulations on your Nature 1st author, this helps a lot. In addition to the publication, you need a strong citation too. Especially you publish in good journals, having a IF>15, means cited at least 15 times on average in a year. So you need to show that your particular paper has also been cited at least like this, or better, more. It is important to establish that you are well-recognized, even for NIW. So show a strong history. This makes the recommendation letter become very important.
Of course NIH senior scientist is an government official. However, from march 2005, there is a rule in NIH that no one can write reference letter for the purpose of supporting GC application. Not even on personal letterhead. Well, you will always hear that people get letter from them, and I know some NIH guys still send out letters. But don't be surprised that they won't.
Based on these, NIW will be a very strong case for you. EB1-OR will be shaky, if all the strong points has been shown to us.
Finall good luck