The Princeton University Library has a collection of several hundred medieval manuscripts, described on the Web page of its Manuscripts Division.
Corsair (Pierpont Morgan Library) catalog of the Morgan Library's collections in New York City. The Morgan has an excellent collection of medieval and renaissance manuscripts.
Catalogue of medieval and Renaissance manuscripts in the Beinecke Rare Book and Manuscript Library, Yale University / by Barbara A. Shailor.
Binghamton, N.Y. : Medieval & Renaissance Texts & Studies, 1984-1992.
Alex Z6621.B4213 1984 v.1-4, Art v.1-2;
The Free Library of Philadelphia has 255 codices and 2000 individual leaves of medieval and renaissance manuscripts. This collection's main page links to an online tour with many page images and to a search engine.
The University of Pennsylvania Libraries boast a large collection of medieval manuscripts including the library of the Inquisition historian Henry Charles Lea (1825-1909) and the Lawrence J. Schoenberg Collection at the Van Pelt Library.