Querying MySQL and SQL Server from same IDE
there is a lot of options but choosing the right one is up to you, this is some of the options :

1) Adminer: http://www.adminer.org/

2) DBeaver: http://dbeaver.jkiss.org/about/

3)DBVisualizer Free: http://www.dbvis.com/

4) sql developer (but you need to install the plugins first) : http://www.oracle.com/technetwork/developer-tools/sql-developer/downloads/index.html