Long distance buses in Argentina are indeed pretty good, in particular those branded “coche-cama”, “ejecutivo”, etc. Way better than the average European bus, and crazy better than the typical Greyhound in North America.
That said, the trip from Buenos Aires to the north of Patagonia will be around 24 hours, and twice that to the south. To boot, prices are on par with flights if not higher.
Going to Puerto Madryn to see the whales and the peninsula is worth it (check the season, though, I don’t think you can see whales all year round), but other than that there is not a lot to see along the coast (sea and desert and wind, which could be lovely but not for thousands of kilometers). With that in mind, I would suggest flying to Madryn and then to Calafate or Ushuaia and work your way up through the west; or viceversa, fly to Bariloche, work your way down to the south and then fly to Madryn and Buenos Aires.
As for renting a van, this is my experience from three years ago: I wanted my kids to visit family in Bariloche so I wanted to rent a 9/12 seater. I couldn’t find anything below USD 3500 for two weeks.
Finally, just a short mention that there are currently restrictions to foreign exchange. You will likely have no issue getting pesos for your dollars/euros, but going the other way could be complicated. This is very new, so it’s hard to predict how things will be in a couple months.