Need to rebuild Google Maps API and Fusion Tables Maps

What I have is a quite popular online map, and webapp made years ago for a popular videogame. The maps were made with Google Maps API and Google Fusion Table ---------- w Google is retiring FT by the end of the year, so I need a data migration to a new system while keeping the same GMaps functionalities.
Maybe something like GeoJSON can be a solution? Maybe just plain Google Maps API? You are the expert on this!
The map has hundreds of markers with pictures in them, all searchable with checkboxes to hide/show specific groups.
All this is used on a static website and in a few webapps, so we are talking about Javascript and Google Maps API. No PHP or other languages were used, and I would like to keep it this way.
So recap: Javascript - Google Maps API - Google Fusion Tables API