You can check free tool Valentina Studio http://www.valentina-db.com/en/valentina-studio-overview which I think is far superior to other GUI tools.
It works natively (!) on all 3 os: linux, mac and windows
* it works with SQLite as well as with mySQL/mariaDB, PostgreSQL and Valentina DB

It has a lots of advanced tools:
* Diagrams with forward engineering
* Schema Editor, which can change structure of your SQLite tables even if they have records
* Data Editor
* SQL Editor with syntax highlighting and auto-completion
* visual Query Builder
* Import/Export
* SQL Dump
* and many others