What are my best options either taking the train or bus between the two cities....
What are the pros and cons ?
Have you checked and found both services available on the day you want to travel? I would assume there are Sunday buses as well as trains but haven't looked myself.
The following informatiom is based on my observations in 2015, though I did not travel directly between the two cities, and things may have changed.
I think either train or bus would work fine. In Ljubljana the two stations are very close together. In Zagreb they seem to be basically adjacent to each other if you look at a map, but there's no direct connection between them, and you have to walk the long way around. I think it took me at least 10 minutes, and it might have been more than 15. The train station is closer to central Zagreb. However, Zagreb has trams going to both stations and there were always taxis sitting outside the bus station.
It was my impressiontthe Zagreb train station was little used. I don't even know that there's a food source inside, beyond perhaps vending machines. The bus station, by contrast, is a bustling place.
Most folks find trains a bit more comfortable than buses, but Internationa buses are generally quite nice, and I don't know how new Croatian rail coaches are.
It is always my recommendation that international bus tickets be bought ahead of time, because just about every such bus I've taken has headed out nearly full.
Thanks for responding...It was recommended by people that live in Zagreb to take the bus as it is more efficient and very little for breakdowns....Found people to be much more helpful in Zagreb but it is a bigger city and got around on the trams easily...