Considering both MEAN and MERN are full stack javascript frameworks this doesn't seem like a valid question. Do you intend to use both Mongo and MySQL? thats probably a bad idea. Are you going to convert the server side Java into node / express Javascript? I doubt it.
Is your question really should I use React / Angular?
It also sounds like Codeigniter was just the front end part and it would call to the Java API. If that was slow building a new UI won't make it faster. The Java API probably needs to be updated to fix the real performance issues here. My guess would be lots of bad sql queries.