The most complete study of the synagogues in Greece is the book The Synagogues of Greece: A Study of Synagogues in Macedonia and Thrace, by the architect Elias Messinas, who has been studying and documenting Jewish heritage in Greece since the early 1990s.
We are happy to remind readers that the full text of the book is available online.
Based on unpublished archival sources, and detailed architectural surveys and drawings, the book, which has many photos, maps, and architectural drawings, traces the history of the synagogues, the Jewish quarters, and Jewish communities in Greece, from antiquity, through Byzantine and Ottoman times, contemporary history and the Holocaust, when 87% of Greek Jewry was annihilated.
Messinas describes about 100 pre-WW2 synagogues in Greece -- only about a dozen of them still stand today.
The book is the result of nearly two decades of research and in-situ work by Messinas and is based on his Ph.D. dissertation at the National Technical University of Athens and a post-doctoral Ally Kaufmann Fellowship research at the Technion Institute of Technology, Israel.
Messinas for years ran Ko haKehilla, a Newsletter about Greek Jewish heritage. It no longer is active, but its archives are online -- at Kol haKellila. The material may be 10 years and more old (and has not been updated), but there a wealth of resources, news articles, essays, reports and photographs, lists and articles about Jewish heritage sites, as well as a bibliography on Greek Jewish history and heritage sites.