Yeah, clearly your best bet is a Nats uniform. He'll be with the minor league team for a couple months. He'll be with the Nats for years, and even now a Nats uniform isn't too soon. Any minor league uniform will be outdated fast, whereas the Nats uniform will never go out of date even if he signs elsewhere as a FA. If you're looking at the commercial aspect of selling prints, you only have one option, putting him in the new Nats uniform.
The question is, which? I personally would prefer the alternate Red uniform to the home whites. I think it would stand out more. And if you decide not to go with a background, I think the red home uni is the only option. With a background, the red might be too much for the painting, and the main white home uniform work better. Just some random thoughts, I look forward to seeing, and purchasing, your final product on the Harper piece. Quite a stellar piece of art even before it's finished, as I've already stated.