How do I use a custom stopwords filter in the Java Weka API?
First of all you have to prepare a text file for your custom stopwords. Then you can use the following code:

import weka.filters.unsupervised.attribute.StringToWordVector;

StringToWordVector filter = new StringToWordVector(10000);
filter.setStopwords(new File(".../stopwords.txt"));


Hope it will help you.