Skip, welcome to HSBBW. I see you're fairly new here, hopefully you've been lurking awhile and seen how great this site can be.
As to your question, think of the old saying "A bird in the hand is worth two in the bush." Does it apply in your case? Does he want to attend the D3 that much more than the D1? Or, does he prefer to not attend the D1 but is getting an offer from them anyway? Unless you answer YES to either or both of these questions, I can't imagine this being that tough of a choice.
Fit is more important than anything, but it sounds like one of those schools is telling him they think he fits them pretty well. I'd think very hard before deciding to not sign that NLI. If the D3 hasn't courted him to the same degree, does he really want to go there that much more than to the D1 school?