Run this SQL statement in the mysql client, Naivcat, or wherever) to retrieve all the MyISAM tables in your database. Replace value of the name_of_your_db variable with your database name.
SET @DATABASE_NAME = 'name_of_your_db';
SELECT CONCAT('ALTER TABLE `', table_name, '` ENGINE=InnoDB;') AS sql_statements
FROM information_schema.tables AS tb 
WHERE table_schema = @DATABASE_NAME 
ORDER BY table_name DESC;
Then, copy the output and run as a new SQL query.