There are a lot of disappointed reviews, and maybe it's with Fantasy Day Tours? I think four different companies do this tour, or something similar to Balos Beach. We booked the Balos/Gramvousa tour through GE ES Tours in Chania old town, and it was very good. I don't remember the exact company which drove ours, but if you book it through GE ES maybe that's the company?
The office of GE ES is very personable, easy to figure out the different tours. They tend to cost only 35-40 Euros per person.
The tour we took picks you up by bus at a hotel, and they stop at maybe six hotels (we walked to a nearby hotel). The bus drive to the where the boats are docked is maybe an hour, which I found interesting as you see the entire coastal vacation rentals west of Chania -- there are a lot of people who vacation near Chania.
We had about fifteen minutes to use the bathroom, and then boarded a large boat, which held maybe 200 passengers? It had restrooms and a little cafeteria. We talked with people as the boat cruised to Gramvousa. There was enough time in Gramvousa to hike to the top, or to go to the beach. (I'd say much better to wait for the beaches at Balos; we hiked to the top and got beautiful photos.)
Back on the boat, a short time later it stops near Balos Beach. You walk down a ramp, then across maybe 300 meters of rocky coast, to get to the sandy beach that faces the ocean water. Just behind it is Balos Lagoon, shallow and warm. Both are fun to swim in. There is a little food vendor off to one side, and a pay toilet, but I recommend the restrooms and food on the boat. We had about three hours for swimming and exploring, more than enough.
Going back, the boat docked, we walked to the bus, the bus left about three minutes later. It's a long ride back, due to traffic and stops the bus makes to drop people off. But you're seeing Crete. We left at about 8 a.m. and were dropped at the hotel about 6:30 p.m.
Most of these trips take an entire day. If you'd do this by rental car, first you have to find a car rental that will let you drive off-road. Because you're going to duplicate the route the bus took, drive farther to the Balos peninsula, and then drive off-road for a half hour. Then park and walk maybe a half mile downhill to the beaches. The one advantage to that way would be you're up high to take photos as you being the descent. But don't imagine a car rental is going to be a real fast way to do this. I'd guess 1.5 hours driving and 20 minutes walking, minimum.
Take the bus/boat. You meet lots of people, are out on the ocean, get to see the area by bus, have relatively cheap food available, etc. This peninsula is no way convenient to get to, no matter how you go, but we're glad we went.