1, You could eliminate the matchFound flag if you create a label for your outer for loop and call break with this label:

matchLoop: for (final String[] synonymArr : mSynonyms) {
    for (int j = 0; j < synonymArr.length; j++) {
        if (inArr[i].equalsIgnoreCase(synonymArr[j])) {
            inArr[i] = synonymArr[ROOT_WORD];
            break matchLoop;
        }
    }
}

Anyway, I think using labels more or less is bad smell, so try to extract out the loops to separate methods.

2, I'd create at lest a Word class which stores the (root)word and its synonyms. I should result more readable the code in the Synonymiser class too:

public class Word {

    private final String rootWord;

    private final Set<String> synomins;

    public Word(final String rootWord, final Collection<String> synomins) {
        super();
        // TODO: empty String/null check
        this.rootWord = rootWord;
        // TODO: convert the input to lowercase (it helps contains())
        this.synomins = new HashSet<String>(synomins);
        this.synomins.add(rootWord);
    }

    public static Word createWord(final String rootWord, final String... synonims) {
        final List<String> synonimList = Arrays.asList(synonims);
        return new Word(rootWord, synonimList);
    }

    public boolean contains(final String word) {
        // TODO: convert word to lowercase for proper comparison
        if (synomins.contains(word)) {
            return true;
        }
        return false;
    }

    public String getRootWord() {
        return rootWord;
    }
}

1, You could eliminate the matchFound flag if you create a label for your outer for loop and call break with this label:

matchLoop: for (final String[] synonymArr : mSynonyms) {
    for (int j = 0; j < synonymArr.length; j++) {
        if (inArr[i].equalsIgnoreCase(synonymArr[j])) {
            inArr[i] = synonymArr[ROOT_WORD];
            break matchLoop;
        }
    }
}

Anyway, I think using labels is more or less bad smell, so try to extract out the loops to separate methods.

2, I'd create at least a Word class which stores the (root)word and its synonyms. I should result more readable the code in the Synonymiser class too:

public class Word {

    private final String rootWord;

    private final Set<String> synomins;

    public Word(final String rootWord, final Collection<String> synomins) {
        super();
        // TODO: empty String/null check
        this.rootWord = rootWord;
        // TODO: convert the input to lowercase (it helps contains())
        this.synomins = new HashSet<String>(synomins);
        this.synomins.add(rootWord);
    }

    public static Word createWord(final String rootWord, final String... synonims) {
        final List<String> synonimList = Arrays.asList(synonims);
        return new Word(rootWord, synonimList);
    }

    public boolean contains(final String word) {
        // TODO: convert word to lowercase for proper comparison
        if (synomins.contains(word)) {
            return true;
        }
        return false;
    }

    public String getRootWord() {
        return rootWord;
    }
}