Try utilizing dictionaries like so. (This is untested).

Map<Character, Integer> letterMap1 = new HashMap<Character, Integer>();
Map<Character, Integer> letterMap2 = new HashMap<Character, Integer>();

for (int i = 0; i < charArr1.length; i++) {
    if (!letterMap1.containsKey(charArr1[i])) {
        letterMap1.put(charArr1[i], 0);
    }  else {
        letterMap1.put(charArr1[i], letterMap1.get(charrArr1[i]) + 1);
    }
}

for (int i = 0; i < charArr2.length; i++) {
    if (!letterMap2.containsKey(charArr2[i])) {
        letterMap2.put(charArr2[i], 0);
    }  else {
        letterMap2.put(charArr2[i], letterMap2.get(charrArr2[i]) + 1);
    }
}

boolean equivalent = true;

if (letterMap1.size() == letterMap2.size()) {
    for (Character c : letterMap1.keySet()) {
        if (!letterMap2.containsKey(c)) {
            equivalent = false;
            break;
        } else {
            if (letterMap1.get(c) != letterMap2.get(c)) {
                equivalent = false;
                break;
            }
        }
    }
} else {
    equivalent = false;
}

if (equivalent) {
    System.out.println("Yes");
} else {
    System.out.println("No");
}

Try utilizing dictionaries like so. (This is untested).

Map<Character, Integer> letterMap1 = new HashMap<Character, Integer>();
Map<Character, Integer> letterMap2 = new HashMap<Character, Integer>();

for (int i = 0; i < charArr1.length; i++) {
    if (!letterMap1.containsKey(charArr1[i])) {
        letterMap1.put(charArr1[i], 0);
    }  else {
        letterMap1.put(charArr1[i], letterMap1.get(charArr1[i]) + 1);
    }
}

for (int i = 0; i < charArr2.length; i++) {
    if (!letterMap2.containsKey(charArr2[i])) {
        letterMap2.put(charArr2[i], 0);
    }  else {
        letterMap2.put(charArr2[i], letterMap2.get(charArr2[i]) + 1);
    }
}

boolean equivalent = true;

if (letterMap1.size() == letterMap2.size()) {
    for (Character c : letterMap1.keySet()) {
        if (!letterMap2.containsKey(c)) {
            equivalent = false;
            break;
        } else {
            if (letterMap1.get(c) != letterMap2.get(c)) {
                equivalent = false;
                break;
            }
        }
    }
} else {
    equivalent = false;
}

if (equivalent) {
    System.out.println("Yes");
} else {
    System.out.println("No");
}