We don't know either how good a student she is, or how fast a runner she is???
But still two good places to start are the US News ranking of small liberal arts colleges and the results of the last few seasons of NCAA D3 cross country and track programs. That allows you to get a quick look at academic strength/reputation and get a feel for which programs are competitive nationally.
While MIT is indeed one of the strongest schools academically in this group especially for engineering and hard science, there are plenty of amazing colleges in this group. Williams, Amherst, Swarthmore, Haverford, Bowdoin, Middlebury, Carleton, Johns Hopkins, WAsh U, Chicago just to name a few.
If your daughter is a strong runner she may be able to get some admissions help. Also no athletic scholarships, but very generous financial aid if family income below $100k annually. Good luck.