Take a look at the USNews college rankings and pay some attention to the separate list of Liberal Arts Colleges that is separate from the "National" univeristies category. A lot of these are NESCAC schools, in the northeast, and they are full of quite bright kids and some very good athletes. Almost always better athletes than they get credit for.
Or, look at the National rankings and extract the higher ranked schools that you know are not D1.
http://www.ncaa-baseball.com/div3master.htm
Above is a link to the D3 list of baseball programs. Among the best academic schools that I am aware of are Amherst,Williams, Weslyan, Rochester, Chigago, Tufts, Swarthmore, Oberlin, Middlebury, Kenyon, Johns Hopkins, Haverford, Emory, Brandeis, Bowdoin.