We used to take ours by car. You could walk them down in the vehicle bay, (bodega) during the trip. If not she would sleep in the car, with the windows cracked open for some fresh air. There may have been people, walking their dog on board, but can´t be sure.Why don´t you just call or go to Buquebus office on Cordoba near 9 de Julio, or at the terminal, and ask them?
Last year when we made this trip, we asked our vet, and he knew exactly what paperwork we needed. I think he charged us 50 pesos. Ask your vet, and he should know and prepare everything for you. If you don't have a vet, I can give you the name of ours! He's great!
When you get on the boat, if you are bringing your car, you can leave your dog in the car. However, be careful of what level you park on. If you are on the lowest level, it is VERY hot, so I wouldn't recommend leaving your dog in the car. On the upper level, it's not as hot, just really loud. There ARE kennels on the ferry, located on the highest level of the boat. You can bring your dog up, and let him travel with all the other doggies! That's the best bet!
Hope that helps. Its super easy and no problem at all.
Unfortunately, I don't know anything about finding hotels that accept dogs. You may have to call around ahead of time and ask, and make sure they know your dog is small and will be in a crate. Good luck!