You will basically end up citing both the manuscript and the publisher of the facsimile. You would cite the thing that is reproduced first, then a period, then a statement saying it is a facsimile of the autograph score or the first edition, or whatever. Sometimes you can take the facsimile statement straight from the title page, sometimes you'll have to devise your own. You would also add information about the editor or if someone wrote a preface, etc. Then finally, you'd have the place and name of the publisher, and the publication date.
Here is an easy one, where you can pretty much take everything from the title page:
The citation would look something like this:
Brahms, Johannes. Concerto for Violin, Op. 77. Facsimile of the holograph score, with an introduction by Yehudi Menuhin and a foreword by Jon Newsom. Washington, DC: Library of Congress, 1979.
Here is one where you'd need to make up your own statement about it being a facsimile:
The citation will look something like this:
Mozart, Wolfgang Amadeus. Klavierkonzert C-Moll, KV 491. Facsimile of the autograph in the Royal College of Music, London. Commentary by Robert D. Levin. Preface by Colin Lawson. Kassel: Bärenreiter, 2014.
If you have one of the manuscripts that isn't by a single composer, it will be the same idea, just start with the name of the manuscript, something like this:
Il Codice Squarcialupi: MS. Mediceo Palatino 87, Biblioteca laurenziana DI Firenze. 15th century music manuscript, facsimile reproduction in colour with accompanying volume of studies edited by F. Alberto Gallo. Firenze: Giunti Barbera; [Lucca]: Libreria musicale italiana, 1992