Here's a few comments on the field:
The University of Chicago has been hurt by the loss of Catherine Brekus to Harvard--they will hopefully hire a replacement next year, but at the moment the whole program is being run by Curtis Evans--although Evans is great and it's a fantastic place to be in general--and you could probably also spend some time at Northwestern with Orsi.
I'm biased, but I do think Harvard is the best place in the country to do American religious history due to the sheer size of the faculty and their diversity of interests. The dean of the Divinity School, David Hempton, is a historian of transatlantic evangelicalism, and in addition you have David Holland, Catherine Brekus, Ann Braude, Marla Frederick, Jonathan Walton, and the list could go on, especially if you include faculty in history and American Studies.
Princeton University has always had a very strong program, especially in African-American religions, as has Yale--but it might be harder to do early American topics at these places than it used to. Obviously Duke and UNC are also traditionally very strong, but UNC lost Maffly-Kipp and Grant Wacker has retired from Duke. Albanese has also retired from UCSB and Holifield from Emory.
I won't keep going on because I don't have exhaustive knowledge of the field (I'm sure Vanderbilt, Florida State, UVA, etc. are strong, but I'm not very familiar with them), but my strong belief is that the more faculty you can draw from in an institution, the better off you are going there. If there's just one or two faculty, you could be in trouble if someone leaves, doesn't get tenure, etc. Plus, the more faculty, the more students there will be in the area, which will help to shape your project in ways you can't anticipate.
I think it's a little artificial to separate out religion programs from history programs that have strong emphases in American Religious History--for example, some of the most important figures in the field in recent years such as Mark Noll and George Marsden (and a whole slew of historians of American Catholicism; and now Darren Dochuk as well) are in the history or (in the case of Tom Tweed) American Studies departments at Notre Dame--part of this I think is the fact that few of these historians would fit in a Catholic theology department.
Another example: Washington University in St Louis now has a very strong contingent of American religion faculty (Leigh Schmidt, Marie Griffith, Laurie Maffly-Kipp, etc.) in their Danforth Center, but in order to work with them as a doctoral student I think you'd need to go through the history department.
Quick edit: I would also add Boston University to your long list depending on your specialization (if you are interested in world Christianity/missions at all, BU, Yale, and Edinburgh are the three centers). Very strong in mission history (Dana Robert), Jon Roberts would be a great resource in the history department, Stephen Prothero is in religion, and there's a number of potential faculty in the School of Theology. Plus you could take classes across the BTI.