Hello Seirup and welcome to the forum!
I don't find either phrase natural because if people are going to use a 'pleasure' type phrase in a sentence, they could say either 'It's been a pleasure to help you (out)', or 'It's been a pleasure helping you!' I think the 'out' is unnecessary especially in a pretty formal sentence.
On the other hand, there's the short phrase in response to thanks for helping, which is simply 'My pleasure!'.
I expect somebody will have different view.