According to the Online Education Database, the three best online Ph.D. programs are from the University of North Carolina at Chapel Hill, the University of Minnesota - Twin Cities, and the University of Florida. These were rated based on several quantifiable factors, including full-time to part-time faculty ratio, financial aid and years of accreditation, as well as acceptance, retention and graduation rates.
Some of the other well rated online Ph.D. programs include University of Nebraska - Lincoln, Texas A & M university, the University of Alabama, the University of Scranton, and the University of Illinois at Urbana-Champaign.
Different universities are stronger in different fields of study. As such finding a school that is well rated for the desired field of study should be more important than looking for one that is well rated overall. Oedb.org has ratings by program as well as degree level. On the website select Ranking, then select Doctorate and a category and subject. The results are based on faculty, financial aid, accreditation and acceptance, retention, and graduation rates, similar to the overall rankings but limited to programs offering the chosen subject.
Another important consideration is the length of the program and the scheduling of classes. For students working while in an online program, making a choice that can accommodate a full-time work schedule is essential.