Yes thats correct, the busses to Puntarenas don't go to the ferry so you will have to take a cab. But the ride is short and probably there are many people who will do the same so you could even share tha taxi with somebody.
Then you will have to buy the ticket and cross the street to get to the ferry. When you arrive in Paquera there are busses waiting but make sure that you get on the one that goes directly to Montezuma. Other buses I think go to Malpais or to Cobano.
I always took early buses and ferrys so I never had problems. Maybe its true that the last ferry doesn't have any buses waiting...I have no information about that.
What bothered me with the direct bus from San Jose:
It leaves at 6 am, you have to be at the bus (I think its Coca Cola bus terminal) very early because there are many people waiting to go to Montezuma.
Even though it leaves at 6, you will be on the ferry that leaves at 9!! So it takes three hours even though the bus normally needs maybe 1,5 hours for the way. But: the bus stops somewhere near Orotina where you can have a breakfast or just a coffee.
When you leave the ferry you have to wait for your bus to get off the ferry and to get on the same bus. There are several and one of them goes to Mal Pais/Santa Teresa so you will have to make sure to be on the right bus. When I went, the buses stopped somewhere before Cobano and the driver asked everybody who wants to go to Malpais to go to the other bus and the people from the other bus that wanted to go to Montezuma, came to our bus.
It was fine and easy.
On the way back we were expecting to get on the direct bus in Montezuma. There were many people waiting, some who wanted to catch the direct bus to SJO and some who wanted to go just to Paquera. So I expected 2 buses. But only one came. Which was a small bus that everybody had to get on to go to Cobano. It was completely full, it was hot and dusty and the bus almost colapsed driving up the steep road :-D It was fun it was adventure but I dont recommend that to everybody. The driver then stopped and asked people to get off and to get on a bus that was driving behind us. So everybody went with 2 buses to Cobano and there we finally could get onto the direct bus to San Jose. This time the bus did not go with us on the ferry. So we had to get on another bus in Puntarenas which was almost full so my brother and me we didn't have the chance to sit next to each other. But no problem. The bus then, instead of taking the new "highway" via Caldera to San Jose, took the old road. In total the way was too long at the end and I was completely tired when I arrived at home.
Thats why I had better experiences taking the not-direct buses :-) The connection is easy and fast and the only thing is that yoy will have to take a cab to get to the ferry.
Both ways are fine though and both have advantages and disadvantages...
When you arrive in Puntarenas after 5, the later buses Puntarenas- San Jose don't go the new route via Caldera, so it takes longer.