First you need to determine how the Works Cited entry will appear. This depends on whether your paper will predominantly reference passages by Milton or alternatively notes (or other material) added by the editors. If the former, then what you gave is about right:
Milton, John. Paradise Lost. Eds. William Kerrigan et al. New York: Random House, 2007.
If on the other hand you mainly are citing the editors' comments, then the Works Cited entry should be under the editor's name:
Kerrigan, William, et al., eds. Paradise Lost. By John Milton. New York: Random House, 2007.
The in-text citation will depend a bit on this too. In the predominately-editor case, the initial reference to the work, in keeping with MLA style, uses the editor's name in text and omits it in the parentheses which give the page number of the footnote:
Kerrigan et al. observe that blah, blah, blah (107).
I'm not sure if the MLA has rules about citing that the location is in a footnote; in this context I don't think it's necessary to have the citation give that detail since you are citing generally the editor and not the underlying author.
On the other hand, if you are citing Milton mostly and the editor material is incidental, you should probably include that detail, as:
This couplet is ambiguous, though; Kerrigan et al. observe that blah, blah, blah (Milton 107 note).