I am aware of US News which publishes the rankings for US Universities every year. But somehow I feel that they try to emphasize more on private universities than public(state) universities. Also they have recently stopped showing the rankings according to fields of study(CS, ECE, Mechanical, etc) without paying them. Google also could not help me find any reliable ranking organisation. I would like to know whether there is any respectable ranking organisation other than US News.
Both of these organisations are International but you can search by region and study area.
The Times Higher Education rankings are compiled by the Times Higher Education magazine in the UK with the help of Thomson Reuters. According to their site
rankings employ 13 carefully calibrated performance indicators to provide the most comprehensive and balanced comparisons available, which are trusted by students, academics, university leaders, industry and governments.
If your goal is a general list, @gman's answer, as well as other general guides, will do.
If your goal is to select a graduate program to apply for, I recommend phds.org. You can specify which criteria are most important to you: research productivity, support for graduate students, diversity, funding, etc. Based on your choices, you will get a personalized ranking of the graduate programs in your area.