Given the recent threads about best D3 baseball programs, the NCSA website (link below) has what it calls a proprietary way of ranking the college baseball programs (4 year) at all levels. The website has a useful filter where you can sort by the various divisions or leave them all combined. The highest rated program from D3 is Johns Hopkins and UC-San Diego is the highest rated D2. Both schools appear in the overall top 50 programs, and others like Emory and MIT appear in the overall top 100.
Rankings and ranking systems are always controversial and no doubt subject to debate. This ranking appears to be more heavily weighted to the schools academic ranking than winning records. Nevertheless, since almost all of the kids playing college baseball at any level will not make a living playing baseball after college, it does make sense to factor in how important academics and the graduation rates are when evaluating programs.