You will see that the pick up and drop off time are well noted in each of the cruise itinerary. Generally speaking, most cruise trip will start at noontime, thus if you are leaving from Hanoi, you will need to depart between 8:00 and 8:30AM to meet the cruise schedule. If you book a seat on the shuttle bus provided by the cruise, you will be picked up from your hotel in this time range or asked to come to a meeting point near the Old Quarter (except for Syrena Cruise whose pick up point is near the West Lake).
The cruise trip will return to the harbor by 11 AM or 12 PM on the last day of the trip and you can expect to reach your hotel between 4:00 and 4:30PM. Day trip to Halong Bay will have later drop off time, at 8:00 PM approximately.
Keep in mind this time range and plan your travel accordingly. For example if you arrive at Hanoi airport at 9:30AM, it will be too late for a cruise departing on the same day. Similarly, any onward flight or train trip from Hanoi will need to be later than 7PM so that you can avoid all the hassle involved.