MySQL query browser limits the number of records to be displayed for performance reasons, because it is an interactive program and nobody like to wait for half an hour before the program crashes with an out-of-memory error. You can change these limits in the settings.
Your Java program will face similar problems.
When using large datasets it is important to plan how you are going to access that dataset and create the necessary indexes.
It would be useful to edit the question to show the structure of the data. Generqlly it looks like this :
CREATE INDEX idx_customer_name ON customer (name);
Here are more details
If you just want to dump the data to work on the data using Excel you can try this on the commandline
mysqldump -u [username] -p -t -T/path/to/directory [database] --fields-enclosed-by=\" --fields-terminated-by=,
In my experience this is a very painful exercise as Excel really is not made to deal with this amount of rows, and the dump format usually is slightly, but infuriatingly incompatible.
Your best bet is to invest an hour of your time to go through a SQL tutorial like sql fundamentals and play with MySQL query browser to get a feel of what you can do with SQL. I guarantee your investment paid itself back by tomorrow.