I had the same problem in hamcrest 1.3 and solved it by writing a matcher, that follows the code of the IsEqual-Matcher but uses a given Comparator instead of Object#equals().
import org.hamcrest.BaseMatcher;
import org.hamcrest.Description;
import org.hamcrest.Factory;
import org.hamcrest.Matcher;
import org.junit.Assert;
import java.lang.reflect.Array;
import java.util.Comparator;
/**
 * Is the value equal to another value, as tested by the
 * given Comparator?<br/>
 * Based on the example of {@link org.hamcrest.core.IsEqual}.
 *
 * @author Serhat Cinar
 */
public class IsEqualWithComparator<T> extends BaseMatcher<T> {
    private final Object expectedValue;
    private final Comparator<T> comparator;
    public IsEqualWithComparator(T equalArg, Comparator<T> comparator) {
        expectedValue = equalArg;
        this.comparator = comparator;
    }
    @Override
    public boolean matches(Object actualValue) {
        return areEqual(actualValue, expectedValue, comparator);
    }
    @Override
    public void describeTo(Description description) {
        description.appendValue(expectedValue);
    }
    private static boolean areEqual(Object actual, Object expected, Comparator comparator) {
        if (actual == null) {
            return expected == null;
        }
        if (expected != null && isArray(actual)) {
            return isArray(expected) && areArraysEqual(actual, expected, comparator);
        }
        return comparator.compare(actual, expected) == 0;
    }
    private static boolean areArraysEqual(Object actualArray, Object expectedArray, Comparator comparator) {
        return areArrayLengthsEqual(actualArray, expectedArray) && areArrayElementsEqual(actualArray, expectedArray, comparator);
    }
    private static boolean areArrayLengthsEqual(Object actualArray, Object expectedArray) {
        return Array.getLength(actualArray) == Array.getLength(expectedArray);
    }
    private static boolean areArrayElementsEqual(Object actualArray, Object expectedArray, Comparator comparator) {
        for (int i = 0; i < Array.getLength(actualArray); i++) {
            if (!areEqual(Array.get(actualArray, i), Array.get(expectedArray, i), comparator)) {
                return false;
            }
        }
        return true;
    }
    private static boolean isArray(Object o) {
        return o.getClass().isArray();
    }
    @Factory
    public static <T> Matcher<T> equalTo(T operand, Comparator<T> comparator) {
        return new IsEqualWithComparator<>(operand, comparator);
    }
    public static void main(String argv[]) {
        Assert.assertThat("abc", IsEqualWithComparator.equalTo("ABC", new Comparator<String>() {
            @Override
            public int compare(String o1, String o2) {
                return o1.equalsIgnoreCase(o2) ? 0 : -1;
            }
        }));
    }
}