Bludevil_bk,
I always look at these kinds of questions from two perspectives. One perspective is for academics and the other perspective is baseball. I find it interesting that yout threw out baseball stats, but no academic stats. Academic stats will be absolutely key in determing possible fits for D3 schools. Keep in mind, it is difficult to recommend or discuss a D3 school without knowing academic performance, and interests.
Also, I'm curious why you are considering only D2/D3 schools since your son is a rising junior. Junior year is a big one, and a lot of things can change quickly if he has the right opportunities (ie travel team, showcase events, etc...) and coaching.
To answer part of your question directly, there are many, many D3 schools in VA, NC, MD, DE, PA, NJ. I suggest you look through this list by region and playoff history (URL below) to get a feel for some of the more successful programs by location. You can then cross-reference these schools by looking at their admissions & tuition info at College Board. This will give you a starting point for D3.
For D2 teams and rankings, I would look through Boyds' World (URL below) and cross reference with College Board.
http://www.d3baseball.com/http://www.collegeboard.com/http://www.boydsworld.com/Feel free to drop me a PM if you want to discuss specifics.