Yes. The 3% is subject to HST. However, the HST is not paid to your municipality. Please remit your HST as per usual to Revenue Canada.
For example, if your accommodation costs $200 per night, plus a three percent marketing levy ($6), plus 15 percent HST ($30.90), the total cost to the consumer would be $236.90 per night. You would remit $6 to your municipality and $30.90 to Revenue Canada.