Music Theory Spectrum
Official print journal of the Society for Music Theory. Features articles and book reviews on a range of topics in music theory and analysis, including aesthetics, the history of theory, linear analysis, post-tonal theory, and narratology.
http://www.ucpressjournals.com/journalSoc.asp?jIssn=0195-6167

Integral Journal
Intégral is a peer-reviewed music theory publication from the Eastman School of Music.
http://theory.esm.rochester.edu/integral/

Music Theory Online
The online journal of the Society for Music Theory.
http://mto.societymusictheory.org/

Theory and Practice
Annual publication by the Music Theory Society of New York State.
http://www.ithaca.edu/music/mtsnys/t&p.html

Journal of Music Theory Pedagogy
Bi-Annual publication covering educational topics in music theory.
http://music.ou.edu/publications/jmtp/index.html